diff --git a/.Dockerignore b/.Dockerignore new file mode 100644 index 00000000..e69de29b diff --git a/.Rprofile b/.Rprofile index a44306b3..6f649330 100644 --- a/.Rprofile +++ b/.Rprofile @@ -1,6 +1,2 @@ -# Configure BioCManager to use Posit Public Package Manager: -options(BioC_mirror = "https://p3m.dev/bioconductor") -options(BIOCONDUCTOR_CONFIG_FILE = "https://p3m.dev/bioconductor/config.yaml") - # activate renv source("renv/activate.R") diff --git a/.github/workflows/build-docker.yaml b/.github/workflows/build-docker.yaml index 4b9f0444..b425414a 100644 --- a/.github/workflows/build-docker.yaml +++ b/.github/workflows/build-docker.yaml @@ -1,18 +1,18 @@ -name: Build scpca-tools image +name: Build scpca-tools images on: push: branches: - main tags: - - 'v*' + - "v*" pull_request: branches: - main env: REGISTRY: ghcr.io - IMAGE_NAME: alexslemonade/scpca-tools + REGISTRY_USER: alexslemonade jobs: build_and_push: @@ -20,12 +20,26 @@ jobs: permissions: contents: read packages: write + strategy: + fail-fast: false + matrix: + include: + - image_name: scpcatools + dockerfile: Dockerfile + - image_name: scpcatools-slim + dockerfile: scpcatools_slim.Dockerfile + - image_name: scpcatools-reports + dockerfile: scpcatools_reports.Dockerfile + - image_name: scpcatools-scvi + dockerfile: scpcatools_scvi.Dockerfile + - image_name: scpcatools-seurat + dockerfile: scpcatools_seurat.Dockerfile steps: - name: Set up Docker Buildx - uses: docker/setup-buildx-action@v2 + uses: docker/setup-buildx-action@v3 - name: Docker login - uses: docker/login-action@v2 + uses: docker/login-action@v3 with: registry: ${{ env.REGISTRY }} username: ${{ github.actor }} @@ -33,16 +47,17 @@ jobs: - name: Docker metadata id: meta - uses: docker/metadata-action@v4 + uses: docker/metadata-action@v5 with: - images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }} + images: ${{ env.REGISTRY }}/${{ env.REGISTRY_USER }}/${{ matrix.image_name }} tags: | type=semver,pattern={{raw}} type=edge,branch=main - - uses: docker/build-push-action@v4 + - uses: docker/build-push-action@v5 with: context: "{{defaultContext}}:docker" + file: ${{ matrix.dockerfile }} push: ${{ github.event_name == 'push' }} tags: ${{ steps.meta.outputs.tags }} labels: ${{ steps.meta.outputs.labels }} diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index ff20b3e6..50b87eaa 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,15 +1,15 @@ # All available hooks: https://pre-commit.com/hooks.html # R specific hooks: https://github.com/lorenzwalthert/precommit repos: -- repo: https://github.com/lorenzwalthert/precommit - rev: v0.3.2.9027 + - repo: https://github.com/lorenzwalthert/precommit + rev: v0.4.2 hooks: - - id: style-files + - id: style-files args: [--style_pkg=styler, --style_fun=tidyverse_style] - # codemeta must be above use-tidy-description when both are used - # - id: codemeta-description-updated - - id: use-tidy-description - - id: spell-check + # codemeta must be above use-tidy-description when both are used + # - id: codemeta-description-updated + - id: use-tidy-description + - id: spell-check exclude: > (?x)^( .*\.[rR]| @@ -35,22 +35,24 @@ repos: (.*/|)DESCRIPTION| (.*/|)NAMESPACE| (.*/|)renv/settings\.dcf| - (.*/|)renv\.lock| - (.*/|)requirements\.txt| - (.*/|)Dockerfile| + (.*/|)renv.*\.lock| + (.*/|)requirements.*\.in| + (.*/|)requirements.*\.txt| + (.*/|).*Dockerfile| (.*/|)WORDLIST| \.github/workflows/.*| data/.*| )$ - - id: lintr - - id: parsable-R - - id: no-browser-statement - - id: no-debug-statement - - id: deps-in-desc -- repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.5.0 + - id: lintr + - id: parsable-R + - id: no-browser-statement + - id: no-debug-statement + - id: deps-in-desc + exclude: docker/.* + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.6.0 hooks: - - id: check-added-large-files - args: ['--maxkb=200'] - - id: end-of-file-fixer + - id: check-added-large-files + args: ["--maxkb=200"] + - id: end-of-file-fixer exclude: '\.Rd' diff --git a/docker/Dockerfile b/docker/Dockerfile index 0e003004..518d6eff 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -1,11 +1,7 @@ -FROM rocker/r-ver:4.3.3 +FROM bioconductor/r-ver:3.18 LABEL maintainer="ccdl@alexslemonade.org" LABEL org.opencontainers.image.source https://github.com/AlexsLemonade/scpcaTools -COPY scripts/install_scpca_deps.sh . - -RUN bash ./install_scpca_deps.sh - #### R packages # Use renv for R packages ENV RENV_CONFIG_CACHE_ENABLED FALSE @@ -15,14 +11,15 @@ WORKDIR /usr/local/renv COPY renv.lock renv.lock # restore renv and remove cache files RUN Rscript -e "renv::restore()" && \ - rm -rf ~/.cache/R/renv && \ - rm -rf /tmp/downloaded_packages && \ - rm -rf /tmp/Rtmp* + rm -rf ~/.cache/R/renv && \ + rm -rf /tmp/downloaded_packages && \ + rm -rf /tmp/Rtmp* # Complete installation of zellkonverter conda env ENV BASILISK_EXTERNAL_DIR /usr/local/renv/basilisk RUN Rscript -e "proc <- basilisk::basiliskStart(env = zellkonverter::zellkonverterAnnDataEnv(), testload = 'anndata'); \ - basilisk::basiliskStop(proc)" + basilisk::basiliskStop(proc); \ + basilisk.utils::cleanConda()" #### Python packages COPY requirements.txt requirements.txt diff --git a/docker/README.md b/docker/README.md index c276a7ba..16e3ddf4 100644 --- a/docker/README.md +++ b/docker/README.md @@ -5,11 +5,34 @@ The image is built from a versioned Rocker image, with additional R packages and It can be built with the following command run in this directory: ``` -docker buildx build . -t scpca-tools --platform linux/amd64 +docker buildx build . -t scpcatools --platform linux/amd64 ``` -Note that this image does not include RStudio, in attempt to make the image smaller. +Note that this image does not include RStudio, in attempt to make the image smaller. This image is built automatically on every update to `scpcaTools` (`main`) and pushed to `ghcr.io/alexslemonade/scpca-tools:edge`. -Release versions of `scpcaTools` will be tagged as `ghcr.io/alexslemonade/scpca-tools:latest` and tagged by version number. +Release versions of `scpcaTools` will be tagged as `ghcr.io/alexslemonade/scpcatools:latest` and tagged by version number. + +The main image includes all of the recommended packages for `scpcaTools` (aside from those only required for development), as well as the Python `scanpy` and `scvi-tools` packages and dependencies. + +There are also smaller images that can be built, which include only the R packages required for `scpcaTools`, with particular additions for specific purposes. These include: + +- `scpcatools_slim.Dockerfile`: A smaller image that includes only the required R packages for `scpcaTools`, with no additional packages. +- `scpcatools_scvi.Dockerfile`: The slim package with the addition of the `zellkonverter` package for reading and writing `AnnData` objects, and the Python `anndata` and `scvi` packages. +- `scpcatools_reports.Dockerfile`: The slim package with the addition `rmarkdown` and `ComplexHeatmap` and associated packages for generating reports. +- `scpcatools_seurat.Dockerfile`: The slim package with the addition `Seurat`. + +These images are built automatically on every update to `scpcaTools` (`main`) and pushed to `ghcr.io/alexslemonade/scpcatool-slims:edge` and `ghcr.io/alexslemonade/scpcatools-scvi:edge`, etc. + +## Generating R and Python dependency files + +Dependency lock files, with the exception of `renv.lock`, are built using the `make-requirements.sh` script. +This script depends on `pip-tools` and should be run using Python 3.10 to match the default version of Python in the Docker images. +For convenience, a conda `environment.yml` file is included in this directory that can be used to create an `scpcatools-dev` environment with the necessary Python version and packages. + +This script will generate the `requirements_*.txt` and `renv_*.lock` files for each set of Python packages to be installed within the various Docker images. +- The requirements files are based on `requirements_*.in` files that specify the high-level package requirements for each image. +- The `renv_*.lock` files are strict subsets of the main `renv.lock` file that is use for development and for the full image. + - The main `renv.lock` file should be updated manually using `renv::snapshot()` from within the `scpcaTools` project. + - After updating `renv.lock`, the `make-requirements.sh` script should be run to update the `renv_*.lock` files. diff --git a/docker/environment.yml b/docker/environment.yml new file mode 100644 index 00000000..7e1c8357 --- /dev/null +++ b/docker/environment.yml @@ -0,0 +1,7 @@ +name: scpcatools-dev +channels: + - conda-forge + - defaults +dependencies: + - python=3.10 + - pip-tools diff --git a/docker/make-requirements.sh b/docker/make-requirements.sh new file mode 100644 index 00000000..5e5c24a3 --- /dev/null +++ b/docker/make-requirements.sh @@ -0,0 +1,26 @@ +#!/bin/bash +set -euo pipefail +# This script is used to generate or update requirements/lock files for R and Python packages +# Requires that the `pip-tools` python package is installed. +# Before running, make sure that the renv.lock file and installed libaries are +# consistent with renv::snapshot() or renv::restore() + +# Set the working directory to the directory of this file +cd "$(dirname "${BASH_SOURCE[0]}")" + +# Python package lists +pip-compile --no-annotate --strip-extras --output-file=requirements.txt requirements.in +pip-compile --no-annotate --strip-extras --output-file=requirements_anndata.txt requirements_anndata.in +pip-compile --no-annotate --strip-extras --output-file=requirements_scvi.txt requirements_scvi.in + +# slim lockfile +Rscript scripts/make-lockfile.R -f renv_slim.lock + +# reports lockfile +Rscript scripts/make-lockfile.R -f renv_reports.lock -p ComplexHeatmap,ggforce,kableExtra,rmarkdown + +# zellkonverter lockfile +Rscript scripts/make-lockfile.R -f renv_zellkonverter.lock -p zellkonverter + +# Seurat lockfile +Rscript scripts/make-lockfile.R -f renv_seurat.lock -p Seurat diff --git a/docker/renv.lock b/docker/renv.lock index 9681d571..c69ddcdf 100644 --- a/docker/renv.lock +++ b/docker/renv.lock @@ -2,26 +2,6 @@ "R": { "Version": "4.3.3", "Repositories": [ - { - "Name": "BioCsoft", - "URL": "https://p3m.dev/bioconductor/packages/3.18/bioc" - }, - { - "Name": "BioCann", - "URL": "https://p3m.dev/bioconductor/packages/3.18/data/annotation" - }, - { - "Name": "BioCexp", - "URL": "https://p3m.dev/bioconductor/packages/3.18/data/experiment" - }, - { - "Name": "BioCworkflows", - "URL": "https://p3m.dev/bioconductor/packages/3.18/workflows" - }, - { - "Name": "BioCbooks", - "URL": "https://p3m.dev/bioconductor/packages/3.18/books" - }, { "Name": "CRAN", "URL": "https://p3m.dev/cran/latest" @@ -36,7 +16,6 @@ "Package": "AnnotationDbi", "Version": "1.64.1", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "Biobase", "BiocGenerics", @@ -56,7 +35,6 @@ "Package": "AnnotationFilter", "Version": "1.26.0", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "GenomicRanges", "R", @@ -70,7 +48,6 @@ "Package": "AnnotationHub", "Version": "3.10.1", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "AnnotationDbi", "BiocFileCache", @@ -102,7 +79,6 @@ "Package": "BSgenome", "Version": "1.70.2", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "BiocGenerics", "BiocIO", @@ -138,7 +114,6 @@ "Package": "BiocFileCache", "Version": "2.10.2", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "DBI", "R", @@ -158,7 +133,6 @@ "Package": "BiocGenerics", "Version": "0.48.1", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "R", "graphics", @@ -195,7 +169,6 @@ "Package": "BiocNeighbors", "Version": "1.20.2", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "BiocParallel", "Matrix", @@ -211,7 +184,6 @@ "Package": "BiocParallel", "Version": "1.36.0", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "BH", "R", @@ -230,7 +202,6 @@ "Package": "BiocSingular", "Version": "1.18.0", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "BiocGenerics", "BiocParallel", @@ -251,7 +222,6 @@ "Package": "BiocVersion", "Version": "3.18.1", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "R" ], @@ -261,7 +231,6 @@ "Package": "Biostrings", "Version": "2.70.3", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "BiocGenerics", "GenomeInfoDb", @@ -294,7 +263,6 @@ "Package": "ComplexHeatmap", "Version": "2.18.0", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "GetoptLong", "GlobalOptions", @@ -415,7 +383,6 @@ "Package": "ExperimentHub", "Version": "2.10.0", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "AnnotationHub", "BiocFileCache", @@ -442,7 +409,6 @@ "Package": "GenomeInfoDb", "Version": "1.38.8", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "BiocGenerics", "GenomeInfoDbData", @@ -461,7 +427,6 @@ "Package": "GenomeInfoDbData", "Version": "1.2.11", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "R" ], @@ -471,7 +436,6 @@ "Package": "GenomicAlignments", "Version": "1.38.2", "Source": "Bioconductor", - "Repository": "Bioconductor 3.18", "Requirements": [ "BiocGenerics", "BiocParallel", @@ -493,7 +457,6 @@ "Package": "GenomicFeatures", "Version": "1.54.4", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "AnnotationDbi", "Biobase", @@ -523,7 +486,6 @@ "Package": "GenomicRanges", "Version": "1.54.1", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "BiocGenerics", "GenomeInfoDb", @@ -568,7 +530,6 @@ "Package": "HDF5Array", "Version": "1.30.1", "Source": "Bioconductor", - "Repository": "Bioconductor 3.18", "Requirements": [ "BiocGenerics", "DelayedArray", @@ -591,7 +552,6 @@ "Package": "IRanges", "Version": "2.36.0", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "BiocGenerics", "R", @@ -607,7 +567,6 @@ "Package": "KEGGREST", "Version": "1.42.0", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "Biostrings", "R", @@ -674,7 +633,6 @@ "Package": "ProtGenerics", "Version": "1.34.0", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "methods" ], @@ -902,7 +860,6 @@ "Package": "ResidualMatrix", "Version": "1.12.0", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "DelayedArray", "Matrix", @@ -915,7 +872,6 @@ "Package": "Rgraphviz", "Version": "2.46.0", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "R", "grDevices", @@ -932,7 +888,6 @@ "Package": "Rhdf5lib", "Version": "1.24.2", "Source": "Bioconductor", - "Repository": "Bioconductor 3.18", "Requirements": [ "R" ], @@ -949,7 +904,6 @@ "Package": "Rhtslib", "Version": "2.4.1", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "zlibbioc" ], @@ -993,7 +947,6 @@ "Package": "S4Arrays", "Version": "1.2.1", "Source": "Bioconductor", - "Repository": "Bioconductor 3.18", "Requirements": [ "BiocGenerics", "IRanges", @@ -1011,7 +964,6 @@ "Package": "S4Vectors", "Version": "0.40.2", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "BiocGenerics", "R", @@ -1148,7 +1100,6 @@ "Package": "SingleR", "Version": "2.4.1", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "BiocNeighbors", "BiocParallel", @@ -1171,7 +1122,6 @@ "Package": "SparseArray", "Version": "1.2.4", "Source": "Bioconductor", - "Repository": "Bioconductor 3.18", "Requirements": [ "BiocGenerics", "IRanges", @@ -1226,7 +1176,6 @@ "Package": "XVector", "Version": "0.42.0", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "BiocGenerics", "IRanges", @@ -1285,7 +1234,6 @@ "Package": "basilisk", "Version": "1.14.3", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "basilisk.utils", "dir.expiry", @@ -1300,7 +1248,6 @@ "Package": "basilisk.utils", "Version": "1.14.1", "Source": "Bioconductor", - "Repository": "Bioconductor 3.18", "Requirements": [ "dir.expiry", "methods", @@ -1313,7 +1260,6 @@ "Package": "batchelor", "Version": "1.18.1", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "BiocGenerics", "BiocNeighbors", @@ -1341,7 +1287,6 @@ "Package": "beachmat", "Version": "2.18.1", "Source": "Bioconductor", - "Repository": "Bioconductor 3.18", "Requirements": [ "BiocGenerics", "DelayedArray", @@ -1369,7 +1314,6 @@ "Package": "biomaRt", "Version": "2.58.2", "Source": "Bioconductor", - "Repository": "Bioconductor 3.18", "Requirements": [ "AnnotationDbi", "BiocFileCache", @@ -1432,7 +1376,6 @@ "Package": "bluster", "Version": "1.12.0", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "BiocNeighbors", "BiocParallel", @@ -1539,7 +1482,6 @@ "Package": "celldex", "Version": "1.12.0", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "AnnotationDbi", "AnnotationHub", @@ -1921,7 +1863,6 @@ "Package": "edgeR", "Version": "4.0.16", "Source": "Bioconductor", - "Repository": "Bioconductor 3.18", "Requirements": [ "R", "Rcpp", @@ -1938,7 +1879,6 @@ "Package": "eds", "Version": "1.4.0", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "Matrix", "Rcpp" @@ -1949,7 +1889,6 @@ "Package": "eisaR", "Version": "1.14.1", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "BiocGenerics", "GenomicRanges", @@ -1981,7 +1920,6 @@ "Package": "ensembldb", "Version": "2.26.0", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "AnnotationDbi", "AnnotationFilter", @@ -2068,7 +2006,6 @@ "Package": "fishpond", "Version": "2.8.0", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "GenomicRanges", "IRanges", @@ -2735,7 +2672,6 @@ "Package": "interactiveDisplayBase", "Version": "1.40.0", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "BiocGenerics", "DT", @@ -3040,7 +2976,6 @@ "Package": "metapod", "Version": "1.10.1", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "Rcpp" ], @@ -3067,7 +3002,6 @@ "Package": "miQC", "Version": "1.10.0", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "R", "SingleCellExperiment", @@ -3170,7 +3104,6 @@ "Package": "ontoProc", "Version": "1.24.0", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "AnnotationHub", "Biobase", @@ -3627,12 +3560,9 @@ "renv": { "Package": "renv", "Version": "1.0.7", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "utils" - ], - "Hash": "397b7b2a265bc5a7a06852524dabae20" + "OS_type": null, + "Repository": "CRAN", + "Source": "Repository" }, "reprex": { "Package": "reprex", @@ -3711,7 +3641,6 @@ "Package": "rhdf5", "Version": "2.46.1", "Source": "Bioconductor", - "Repository": "Bioconductor 3.18", "Requirements": [ "R", "Rhdf5lib", @@ -3725,7 +3654,6 @@ "Package": "rhdf5filters", "Version": "1.14.1", "Source": "Bioconductor", - "Repository": "Bioconductor 3.18", "Requirements": [ "Rhdf5lib" ], @@ -3885,7 +3813,6 @@ "Package": "scater", "Version": "1.30.1", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "BiocGenerics", "BiocNeighbors", @@ -3934,7 +3861,6 @@ "Package": "scran", "Version": "1.30.2", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "BH", "BiocGenerics", @@ -4548,7 +4474,6 @@ "Package": "tximport", "Version": "1.30.0", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "methods", "stats", @@ -4757,7 +4682,6 @@ "Package": "zellkonverter", "Version": "1.12.1", "Source": "Bioconductor", - "Repository": "RSPM", "Requirements": [ "DelayedArray", "Matrix", @@ -4776,7 +4700,6 @@ "Package": "zlibbioc", "Version": "1.48.2", "Source": "Bioconductor", - "Repository": "RSPM", "Hash": "2344be62c2da4d9e9942b5d8db346e59" }, "zoo": { diff --git a/docker/renv_reports.lock b/docker/renv_reports.lock new file mode 100644 index 00000000..815c9e62 --- /dev/null +++ b/docker/renv_reports.lock @@ -0,0 +1,1574 @@ +{ + "R": { + "Version": "4.3.3", + "Repositories": [ + { + "Name": "BioCsoft", + "URL": "https://bioconductor.org/packages/3.18/bioc" + }, + { + "Name": "BioCann", + "URL": "https://bioconductor.org/packages/3.18/data/annotation" + }, + { + "Name": "BioCexp", + "URL": "https://bioconductor.org/packages/3.18/data/experiment" + }, + { + "Name": "BioCworkflows", + "URL": "https://bioconductor.org/packages/3.18/workflows" + }, + { + "Name": "BioCbooks", + "URL": "https://bioconductor.org/packages/3.18/books" + }, + { + "Name": "CRAN", + "URL": "https://p3m.dev/cran/latest" + } + ] + }, + "Bioconductor": { + "Version": "3.18" + }, + "Packages": { + "BH": { + "Package": "BH", + "Version": "1.84.0-0", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "a8235afbcd6316e6e91433ea47661013" + }, + "Biobase": { + "Package": "Biobase", + "Version": "2.62.0", + "Source": "Bioconductor", + "Requirements": [ + "BiocGenerics", + "R", + "methods", + "utils" + ], + "Hash": "38252a34e82d3ff6bb46b4e2252d2dce" + }, + "BiocGenerics": { + "Package": "BiocGenerics", + "Version": "0.48.1", + "Source": "Repository" + }, + "BiocManager": { + "Package": "BiocManager", + "Version": "1.30.22", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "utils" + ], + "Hash": "d57e43105a1aa9cb54fdb4629725acb1" + }, + "BiocNeighbors": { + "Package": "BiocNeighbors", + "Version": "1.20.2", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "BiocParallel", + "Matrix", + "Rcpp", + "RcppHNSW", + "S4Vectors", + "methods", + "stats" + ], + "Hash": "c5c8ade5852fd3b25c66ec28873d00f1" + }, + "BiocParallel": { + "Package": "BiocParallel", + "Version": "1.36.0", + "Source": "Bioconductor", + "Requirements": [ + "BH", + "R", + "codetools", + "cpp11", + "futile.logger", + "methods", + "parallel", + "snow", + "stats", + "utils" + ], + "Hash": "6d1689ee8b65614ba6ef4012a67b663a" + }, + "BiocVersion": { + "Package": "BiocVersion", + "Version": "3.18.1", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "R" + ], + "Hash": "2ecaed86684f5fae76ed5530f9d29c4a" + }, + "ComplexHeatmap": { + "Package": "ComplexHeatmap", + "Version": "2.18.0", + "Source": "Repository" + }, + "DBI": { + "Package": "DBI", + "Version": "1.2.2", + "Source": "Repository" + }, + "DelayedArray": { + "Package": "DelayedArray", + "Version": "0.28.0", + "Source": "Bioconductor", + "Requirements": [ + "BiocGenerics", + "IRanges", + "Matrix", + "MatrixGenerics", + "R", + "S4Arrays", + "S4Vectors", + "SparseArray", + "methods", + "stats", + "stats4" + ], + "Hash": "0e5c84e543a3d04ce64c6f60ed46d7eb" + }, + "DelayedMatrixStats": { + "Package": "DelayedMatrixStats", + "Version": "1.24.0", + "Source": "Bioconductor", + "Requirements": [ + "DelayedArray", + "IRanges", + "Matrix", + "MatrixGenerics", + "S4Vectors", + "methods", + "sparseMatrixStats" + ], + "Hash": "71c2d178d33f9d91999f67dc2d53b747" + }, + "DropletUtils": { + "Package": "DropletUtils", + "Version": "1.22.0", + "Source": "Bioconductor", + "Requirements": [ + "BH", + "BiocGenerics", + "BiocParallel", + "DelayedArray", + "DelayedMatrixStats", + "GenomicRanges", + "HDF5Array", + "IRanges", + "Matrix", + "R.utils", + "Rcpp", + "Rhdf5lib", + "S4Vectors", + "SingleCellExperiment", + "SummarizedExperiment", + "beachmat", + "dqrng", + "edgeR", + "methods", + "rhdf5", + "scuttle", + "stats", + "utils" + ], + "Hash": "be3893d30c97591f1d3ec6f053830c3a" + }, + "GenomeInfoDb": { + "Package": "GenomeInfoDb", + "Version": "1.38.8", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "BiocGenerics", + "GenomeInfoDbData", + "IRanges", + "R", + "RCurl", + "S4Vectors", + "methods", + "stats", + "stats4", + "utils" + ], + "Hash": "155053909d2831bfac154a1118151d6b" + }, + "GenomeInfoDbData": { + "Package": "GenomeInfoDbData", + "Version": "1.2.11", + "Source": "Bioconductor", + "Requirements": [ + "R" + ], + "Hash": "10f32956181d1d46bd8402c93ac193e8" + }, + "GenomicRanges": { + "Package": "GenomicRanges", + "Version": "1.54.1", + "Source": "Bioconductor", + "Requirements": [ + "BiocGenerics", + "GenomeInfoDb", + "IRanges", + "R", + "S4Vectors", + "XVector", + "methods", + "stats", + "stats4", + "utils" + ], + "Hash": "7e0c1399af35369312d9c399454374e8" + }, + "GetoptLong": { + "Package": "GetoptLong", + "Version": "1.0.5", + "Source": "Repository" + }, + "GlobalOptions": { + "Package": "GlobalOptions", + "Version": "0.1.2", + "Source": "Repository" + }, + "HDF5Array": { + "Package": "HDF5Array", + "Version": "1.30.1", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "BiocGenerics", + "DelayedArray", + "IRanges", + "Matrix", + "R", + "Rhdf5lib", + "S4Arrays", + "S4Vectors", + "methods", + "rhdf5", + "rhdf5filters", + "stats", + "tools", + "utils" + ], + "Hash": "9b8deb4fd34fa439c16c829457d1968f" + }, + "IRanges": { + "Package": "IRanges", + "Version": "2.36.0", + "Source": "Repository" + }, + "MASS": { + "Package": "MASS", + "Version": "7.3-60.0.1", + "Source": "Repository" + }, + "Matrix": { + "Package": "Matrix", + "Version": "1.6-5", + "Source": "Repository" + }, + "MatrixGenerics": { + "Package": "MatrixGenerics", + "Version": "1.14.0", + "Source": "Bioconductor", + "Requirements": [ + "matrixStats", + "methods" + ], + "Hash": "088cd2077b5619fcb7b373b1a45174e7" + }, + "R.methodsS3": { + "Package": "R.methodsS3", + "Version": "1.8.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "utils" + ], + "Hash": "278c286fd6e9e75d0c2e8f731ea445c8" + }, + "R.oo": { + "Package": "R.oo", + "Version": "1.26.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "R.methodsS3", + "methods", + "utils" + ], + "Hash": "4fed809e53ddb5407b3da3d0f572e591" + }, + "R.utils": { + "Package": "R.utils", + "Version": "2.12.3", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "R.methodsS3", + "R.oo", + "methods", + "tools", + "utils" + ], + "Hash": "3dc2829b790254bfba21e60965787651" + }, + "R6": { + "Package": "R6", + "Version": "2.5.1", + "Source": "Repository" + }, + "RColorBrewer": { + "Package": "RColorBrewer", + "Version": "1.1-3", + "Source": "Repository" + }, + "RCurl": { + "Package": "RCurl", + "Version": "1.98-1.14", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "bitops", + "methods" + ], + "Hash": "47f648d288079d0c696804ad4e55197e" + }, + "Rcpp": { + "Package": "Rcpp", + "Version": "1.0.12", + "Source": "Repository" + }, + "RcppEigen": { + "Package": "RcppEigen", + "Version": "0.3.4.0.0", + "Source": "Repository" + }, + "RcppHNSW": { + "Package": "RcppHNSW", + "Version": "0.6.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "Rcpp", + "methods" + ], + "Hash": "1f2dc32c27746a35196aaf95adb357be" + }, + "Rhdf5lib": { + "Package": "Rhdf5lib", + "Version": "1.24.2", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "R" + ], + "Hash": "3cf103db29d75af0221d71946509a30c" + }, + "S4Arrays": { + "Package": "S4Arrays", + "Version": "1.2.1", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "BiocGenerics", + "IRanges", + "Matrix", + "R", + "S4Vectors", + "abind", + "crayon", + "methods", + "stats" + ], + "Hash": "3213a9826adb8f48e51af1e7b30fa568" + }, + "S4Vectors": { + "Package": "S4Vectors", + "Version": "0.40.2", + "Source": "Repository" + }, + "SingleCellExperiment": { + "Package": "SingleCellExperiment", + "Version": "1.24.0", + "Source": "Bioconductor", + "Requirements": [ + "BiocGenerics", + "DelayedArray", + "GenomicRanges", + "S4Vectors", + "SummarizedExperiment", + "methods", + "stats", + "utils" + ], + "Hash": "e21b3571ce76eb4dfe6bf7900960aa6a" + }, + "SparseArray": { + "Package": "SparseArray", + "Version": "1.2.4", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "BiocGenerics", + "IRanges", + "Matrix", + "MatrixGenerics", + "R", + "S4Arrays", + "S4Vectors", + "XVector", + "matrixStats", + "methods", + "stats" + ], + "Hash": "391092e7b81373ab624bd6471cebccd4" + }, + "SummarizedExperiment": { + "Package": "SummarizedExperiment", + "Version": "1.32.0", + "Source": "Bioconductor", + "Requirements": [ + "Biobase", + "BiocGenerics", + "DelayedArray", + "GenomeInfoDb", + "GenomicRanges", + "IRanges", + "Matrix", + "MatrixGenerics", + "R", + "S4Arrays", + "S4Vectors", + "methods", + "stats", + "tools", + "utils" + ], + "Hash": "caee529bf9710ff6fe1776612fcaa266" + }, + "XVector": { + "Package": "XVector", + "Version": "0.42.0", + "Source": "Bioconductor", + "Requirements": [ + "BiocGenerics", + "IRanges", + "R", + "S4Vectors", + "methods", + "tools", + "utils", + "zlibbioc" + ], + "Hash": "65c0b6bca03f88758f86ef0aa18c4873" + }, + "abind": { + "Package": "abind", + "Version": "1.4-5", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "methods", + "utils" + ], + "Hash": "4f57884290cc75ab22f4af9e9d4ca862" + }, + "askpass": { + "Package": "askpass", + "Version": "1.2.0", + "Source": "Repository" + }, + "backports": { + "Package": "backports", + "Version": "1.4.1", + "Source": "Repository" + }, + "base64enc": { + "Package": "base64enc", + "Version": "0.1-3", + "Source": "Repository" + }, + "beachmat": { + "Package": "beachmat", + "Version": "2.18.1", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "BiocGenerics", + "DelayedArray", + "Matrix", + "Rcpp", + "SparseArray", + "methods" + ], + "Hash": "c1c423ca7149d9e7f55d1e609342c2bd" + }, + "bit": { + "Package": "bit", + "Version": "4.0.5", + "Source": "Repository" + }, + "bit64": { + "Package": "bit64", + "Version": "4.0.5", + "Source": "Repository" + }, + "bitops": { + "Package": "bitops", + "Version": "1.0-7", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "b7d8d8ee39869c18d8846a184dd8a1af" + }, + "blob": { + "Package": "blob", + "Version": "1.2.4", + "Source": "Repository" + }, + "bluster": { + "Package": "bluster", + "Version": "1.12.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "BiocNeighbors", + "BiocParallel", + "Matrix", + "Rcpp", + "S4Vectors", + "cluster", + "igraph", + "methods", + "stats", + "utils" + ], + "Hash": "fca0d5ffad6380f13cad4d7855107aef" + }, + "broom": { + "Package": "broom", + "Version": "1.0.5", + "Source": "Repository" + }, + "bslib": { + "Package": "bslib", + "Version": "0.7.0", + "Source": "Repository" + }, + "cachem": { + "Package": "cachem", + "Version": "1.0.8", + "Source": "Repository" + }, + "callr": { + "Package": "callr", + "Version": "3.7.6", + "Source": "Repository" + }, + "cellranger": { + "Package": "cellranger", + "Version": "1.1.0", + "Source": "Repository" + }, + "circlize": { + "Package": "circlize", + "Version": "0.4.16", + "Source": "Repository" + }, + "cli": { + "Package": "cli", + "Version": "3.6.2", + "Source": "Repository" + }, + "clipr": { + "Package": "clipr", + "Version": "0.8.0", + "Source": "Repository" + }, + "clue": { + "Package": "clue", + "Version": "0.3-65", + "Source": "Repository" + }, + "cluster": { + "Package": "cluster", + "Version": "2.1.6", + "Source": "Repository" + }, + "codetools": { + "Package": "codetools", + "Version": "0.2-20", + "Source": "Repository" + }, + "colorspace": { + "Package": "colorspace", + "Version": "2.1-0", + "Source": "Repository" + }, + "conflicted": { + "Package": "conflicted", + "Version": "1.2.0", + "Source": "Repository" + }, + "cpp11": { + "Package": "cpp11", + "Version": "0.4.7", + "Source": "Repository" + }, + "crayon": { + "Package": "crayon", + "Version": "1.5.2", + "Source": "Repository" + }, + "curl": { + "Package": "curl", + "Version": "5.2.1", + "Source": "Repository" + }, + "data.table": { + "Package": "data.table", + "Version": "1.15.4", + "Source": "Repository" + }, + "dbplyr": { + "Package": "dbplyr", + "Version": "2.5.0", + "Source": "Repository" + }, + "digest": { + "Package": "digest", + "Version": "0.6.35", + "Source": "Repository" + }, + "doParallel": { + "Package": "doParallel", + "Version": "1.0.17", + "Source": "Repository" + }, + "dplyr": { + "Package": "dplyr", + "Version": "1.1.4", + "Source": "Repository" + }, + "dqrng": { + "Package": "dqrng", + "Version": "0.3.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "BH", + "R", + "Rcpp", + "sitmo" + ], + "Hash": "824df2aeba88d701df5e79018b35b815" + }, + "dtplyr": { + "Package": "dtplyr", + "Version": "1.3.1", + "Source": "Repository" + }, + "edgeR": { + "Package": "edgeR", + "Version": "4.0.16", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "R", + "Rcpp", + "graphics", + "limma", + "locfit", + "methods", + "stats", + "utils" + ], + "Hash": "a0405c7890708dcb53809d46758800f4" + }, + "ellipsis": { + "Package": "ellipsis", + "Version": "0.3.2", + "Source": "Repository" + }, + "evaluate": { + "Package": "evaluate", + "Version": "0.23", + "Source": "Repository" + }, + "fansi": { + "Package": "fansi", + "Version": "1.0.6", + "Source": "Repository" + }, + "farver": { + "Package": "farver", + "Version": "2.1.1", + "Source": "Repository" + }, + "fastmap": { + "Package": "fastmap", + "Version": "1.1.1", + "Source": "Repository" + }, + "fishpond": { + "Package": "fishpond", + "Version": "2.8.0", + "Source": "Bioconductor", + "Requirements": [ + "GenomicRanges", + "IRanges", + "Matrix", + "S4Vectors", + "SingleCellExperiment", + "SummarizedExperiment", + "abind", + "graphics", + "gtools", + "jsonlite", + "matrixStats", + "methods", + "qvalue", + "stats", + "svMisc", + "utils" + ], + "Hash": "60ebe3366ccb6c1a11a99682f56f2a2f" + }, + "flexmix": { + "Package": "flexmix", + "Version": "2.3-19", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "grDevices", + "graphics", + "grid", + "lattice", + "methods", + "modeltools", + "nnet", + "stats", + "stats4", + "utils" + ], + "Hash": "0cb3c4b251c2d3fd5923d3e7e6021ee2" + }, + "fontawesome": { + "Package": "fontawesome", + "Version": "0.5.2", + "Source": "Repository" + }, + "forcats": { + "Package": "forcats", + "Version": "1.0.0", + "Source": "Repository" + }, + "foreach": { + "Package": "foreach", + "Version": "1.5.2", + "Source": "Repository" + }, + "formatR": { + "Package": "formatR", + "Version": "1.14", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R" + ], + "Hash": "63cb26d12517c7863f5abb006c5e0f25" + }, + "fs": { + "Package": "fs", + "Version": "1.6.3", + "Source": "Repository" + }, + "futile.logger": { + "Package": "futile.logger", + "Version": "1.4.3", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "futile.options", + "lambda.r", + "utils" + ], + "Hash": "99f0ace8c05ec7d3683d27083c4f1e7e" + }, + "futile.options": { + "Package": "futile.options", + "Version": "1.0.1", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R" + ], + "Hash": "0d9bf02413ddc2bbe8da9ce369dcdd2b" + }, + "gargle": { + "Package": "gargle", + "Version": "1.5.2", + "Source": "Repository" + }, + "generics": { + "Package": "generics", + "Version": "0.1.3", + "Source": "Repository" + }, + "getopt": { + "Package": "getopt", + "Version": "1.20.4", + "Source": "Repository" + }, + "ggforce": { + "Package": "ggforce", + "Version": "0.4.2", + "Source": "Repository" + }, + "ggplot2": { + "Package": "ggplot2", + "Version": "3.5.0", + "Source": "Repository" + }, + "glue": { + "Package": "glue", + "Version": "1.7.0", + "Source": "Repository" + }, + "googledrive": { + "Package": "googledrive", + "Version": "2.1.1", + "Source": "Repository" + }, + "googlesheets4": { + "Package": "googlesheets4", + "Version": "1.1.1", + "Source": "Repository" + }, + "grDevices": { + "Package": "grDevices", + "Version": "4.3.3", + "Source": "R" + }, + "graphics": { + "Package": "graphics", + "Version": "4.3.3", + "Source": "R" + }, + "grid": { + "Package": "grid", + "Version": "4.3.3", + "Source": "R" + }, + "gtable": { + "Package": "gtable", + "Version": "0.3.5", + "Source": "Repository" + }, + "gtools": { + "Package": "gtools", + "Version": "3.9.5", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "methods", + "stats", + "utils" + ], + "Hash": "588d091c35389f1f4a9d533c8d709b35" + }, + "haven": { + "Package": "haven", + "Version": "2.5.4", + "Source": "Repository" + }, + "highr": { + "Package": "highr", + "Version": "0.10", + "Source": "Repository" + }, + "hms": { + "Package": "hms", + "Version": "1.1.3", + "Source": "Repository" + }, + "htmltools": { + "Package": "htmltools", + "Version": "0.5.8.1", + "Source": "Repository" + }, + "httr": { + "Package": "httr", + "Version": "1.4.7", + "Source": "Repository" + }, + "ids": { + "Package": "ids", + "Version": "1.0.1", + "Source": "Repository" + }, + "igraph": { + "Package": "igraph", + "Version": "2.0.3", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "Matrix", + "R", + "cli", + "cpp11", + "grDevices", + "graphics", + "lifecycle", + "magrittr", + "methods", + "pkgconfig", + "rlang", + "stats", + "utils", + "vctrs" + ], + "Hash": "c3b7d801d722e26e4cd888e042bf9af5" + }, + "isoband": { + "Package": "isoband", + "Version": "0.2.7", + "Source": "Repository" + }, + "iterators": { + "Package": "iterators", + "Version": "1.0.14", + "Source": "Repository" + }, + "jquerylib": { + "Package": "jquerylib", + "Version": "0.1.4", + "Source": "Repository" + }, + "jsonlite": { + "Package": "jsonlite", + "Version": "1.8.8", + "Source": "Repository" + }, + "kableExtra": { + "Package": "kableExtra", + "Version": "1.4.0", + "Source": "Repository" + }, + "knitr": { + "Package": "knitr", + "Version": "1.46", + "Source": "Repository" + }, + "labeling": { + "Package": "labeling", + "Version": "0.4.3", + "Source": "Repository" + }, + "lambda.r": { + "Package": "lambda.r", + "Version": "1.2.4", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "formatR" + ], + "Hash": "b1e925c4b9ffeb901bacf812cbe9a6ad" + }, + "lattice": { + "Package": "lattice", + "Version": "0.22-6", + "Source": "Repository" + }, + "lifecycle": { + "Package": "lifecycle", + "Version": "1.0.4", + "Source": "Repository" + }, + "limma": { + "Package": "limma", + "Version": "3.58.1", + "Source": "Bioconductor", + "Requirements": [ + "R", + "grDevices", + "graphics", + "methods", + "statmod", + "stats", + "utils" + ], + "Hash": "74c3b64358e0be7edc3ecd130816dd3f" + }, + "locfit": { + "Package": "locfit", + "Version": "1.5-9.9", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "lattice" + ], + "Hash": "3885127e04b35dafded049075057ad83" + }, + "lubridate": { + "Package": "lubridate", + "Version": "1.9.3", + "Source": "Repository" + }, + "magrittr": { + "Package": "magrittr", + "Version": "2.0.3", + "Source": "Repository" + }, + "matrixStats": { + "Package": "matrixStats", + "Version": "1.3.0", + "Source": "Repository" + }, + "memoise": { + "Package": "memoise", + "Version": "2.0.1", + "Source": "Repository" + }, + "methods": { + "Package": "methods", + "Version": "4.3.3", + "Source": "R" + }, + "mgcv": { + "Package": "mgcv", + "Version": "1.9-1", + "Source": "Repository" + }, + "miQC": { + "Package": "miQC", + "Version": "1.10.0", + "Source": "Bioconductor", + "Requirements": [ + "R", + "SingleCellExperiment", + "flexmix", + "ggplot2", + "splines" + ], + "Hash": "5d3660451d88509307ce0b0e48748109" + }, + "mime": { + "Package": "mime", + "Version": "0.12", + "Source": "Repository" + }, + "modelr": { + "Package": "modelr", + "Version": "0.1.11", + "Source": "Repository" + }, + "modeltools": { + "Package": "modeltools", + "Version": "0.2-23", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "methods", + "stats", + "stats4" + ], + "Hash": "f5a957c02222589bdf625a67be68b2a9" + }, + "munsell": { + "Package": "munsell", + "Version": "0.5.1", + "Source": "Repository" + }, + "nlme": { + "Package": "nlme", + "Version": "3.1-164", + "Source": "Repository" + }, + "nnet": { + "Package": "nnet", + "Version": "7.3-19", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "stats", + "utils" + ], + "Hash": "2c797b46eea7fb58ede195bc0b1f1138" + }, + "openssl": { + "Package": "openssl", + "Version": "2.1.2", + "Source": "Repository" + }, + "optparse": { + "Package": "optparse", + "Version": "1.7.5", + "Source": "Repository" + }, + "parallel": { + "Package": "parallel", + "Version": "4.3.3", + "Source": "R" + }, + "pillar": { + "Package": "pillar", + "Version": "1.9.0", + "Source": "Repository" + }, + "pkgconfig": { + "Package": "pkgconfig", + "Version": "2.0.3", + "Source": "Repository" + }, + "plyr": { + "Package": "plyr", + "Version": "1.8.9", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "Rcpp" + ], + "Hash": "6b8177fd19982f0020743fadbfdbd933" + }, + "png": { + "Package": "png", + "Version": "0.1-8", + "Source": "Repository" + }, + "polyclip": { + "Package": "polyclip", + "Version": "1.10-6", + "Source": "Repository" + }, + "prettyunits": { + "Package": "prettyunits", + "Version": "1.2.0", + "Source": "Repository" + }, + "processx": { + "Package": "processx", + "Version": "3.8.4", + "Source": "Repository" + }, + "progress": { + "Package": "progress", + "Version": "1.2.3", + "Source": "Repository" + }, + "ps": { + "Package": "ps", + "Version": "1.7.6", + "Source": "Repository" + }, + "purrr": { + "Package": "purrr", + "Version": "1.0.2", + "Source": "Repository" + }, + "qvalue": { + "Package": "qvalue", + "Version": "2.34.0", + "Source": "Bioconductor", + "Requirements": [ + "R", + "ggplot2", + "grid", + "reshape2", + "splines" + ], + "Hash": "76fc42834c44b69e4021f6ade524d299" + }, + "ragg": { + "Package": "ragg", + "Version": "1.3.0", + "Source": "Repository" + }, + "rappdirs": { + "Package": "rappdirs", + "Version": "0.3.3", + "Source": "Repository" + }, + "readr": { + "Package": "readr", + "Version": "2.1.5", + "Source": "Repository" + }, + "readxl": { + "Package": "readxl", + "Version": "1.4.3", + "Source": "Repository" + }, + "rematch": { + "Package": "rematch", + "Version": "2.0.0", + "Source": "Repository" + }, + "rematch2": { + "Package": "rematch2", + "Version": "2.1.2", + "Source": "Repository" + }, + "renv": { + "Package": "renv", + "Version": "1.0.7", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "utils" + ], + "Hash": "397b7b2a265bc5a7a06852524dabae20" + }, + "reprex": { + "Package": "reprex", + "Version": "2.1.0", + "Source": "Repository" + }, + "reshape2": { + "Package": "reshape2", + "Version": "1.4.4", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "Rcpp", + "plyr", + "stringr" + ], + "Hash": "bb5996d0bd962d214a11140d77589917" + }, + "rhdf5": { + "Package": "rhdf5", + "Version": "2.46.1", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "R", + "Rhdf5lib", + "S4Vectors", + "methods", + "rhdf5filters" + ], + "Hash": "b0a244022c3427cd8213c33804c6b5de" + }, + "rhdf5filters": { + "Package": "rhdf5filters", + "Version": "1.14.1", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "Rhdf5lib" + ], + "Hash": "d27a2f6a89def6388fad5b0aae026220" + }, + "rjson": { + "Package": "rjson", + "Version": "0.2.21", + "Source": "Repository" + }, + "rlang": { + "Package": "rlang", + "Version": "1.1.3", + "Source": "Repository" + }, + "rmarkdown": { + "Package": "rmarkdown", + "Version": "2.26", + "Source": "Repository" + }, + "rstudioapi": { + "Package": "rstudioapi", + "Version": "0.16.0", + "Source": "Repository" + }, + "rvest": { + "Package": "rvest", + "Version": "1.0.4", + "Source": "Repository" + }, + "sass": { + "Package": "sass", + "Version": "0.4.9", + "Source": "Repository" + }, + "scales": { + "Package": "scales", + "Version": "1.3.0", + "Source": "Repository" + }, + "scuttle": { + "Package": "scuttle", + "Version": "1.12.0", + "Source": "Bioconductor", + "Requirements": [ + "BiocGenerics", + "BiocParallel", + "DelayedArray", + "DelayedMatrixStats", + "GenomicRanges", + "Matrix", + "Rcpp", + "S4Vectors", + "SingleCellExperiment", + "SummarizedExperiment", + "beachmat", + "methods", + "stats", + "utils" + ], + "Hash": "1412c4b6dfd8de528e1101e493e66a02" + }, + "selectr": { + "Package": "selectr", + "Version": "0.4-2", + "Source": "Repository" + }, + "shape": { + "Package": "shape", + "Version": "1.4.6.1", + "Source": "Repository" + }, + "sitmo": { + "Package": "sitmo", + "Version": "2.0.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "Rcpp" + ], + "Hash": "c956d93f6768a9789edbc13072b70c78" + }, + "snow": { + "Package": "snow", + "Version": "0.4-4", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "utils" + ], + "Hash": "40b74690debd20c57d93d8c246b305d4" + }, + "sparseMatrixStats": { + "Package": "sparseMatrixStats", + "Version": "1.14.0", + "Source": "Bioconductor", + "Requirements": [ + "Matrix", + "MatrixGenerics", + "Rcpp", + "matrixStats", + "methods" + ], + "Hash": "49383d0f6c6152ff7cb594f254c23cc8" + }, + "splines": { + "Package": "splines", + "Version": "4.3.3", + "Source": "R" + }, + "statmod": { + "Package": "statmod", + "Version": "1.5.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "graphics", + "stats" + ], + "Hash": "26e158d12052c279bdd4ba858b80fb1f" + }, + "stats": { + "Package": "stats", + "Version": "4.3.3", + "Source": "R" + }, + "stats4": { + "Package": "stats4", + "Version": "4.3.3", + "Source": "R" + }, + "stringi": { + "Package": "stringi", + "Version": "1.8.3", + "Source": "Repository" + }, + "stringr": { + "Package": "stringr", + "Version": "1.5.1", + "Source": "Repository" + }, + "svMisc": { + "Package": "svMisc", + "Version": "1.2.3", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "methods", + "stats", + "tools", + "utils" + ], + "Hash": "b13f5680860f67c32ccb006ad38f24f4" + }, + "svglite": { + "Package": "svglite", + "Version": "2.1.3", + "Source": "Repository" + }, + "sys": { + "Package": "sys", + "Version": "3.4.2", + "Source": "Repository" + }, + "systemfonts": { + "Package": "systemfonts", + "Version": "1.0.6", + "Source": "Repository" + }, + "textshaping": { + "Package": "textshaping", + "Version": "0.3.7", + "Source": "Repository" + }, + "tibble": { + "Package": "tibble", + "Version": "3.2.1", + "Source": "Repository" + }, + "tidyr": { + "Package": "tidyr", + "Version": "1.3.1", + "Source": "Repository" + }, + "tidyselect": { + "Package": "tidyselect", + "Version": "1.2.1", + "Source": "Repository" + }, + "tidyverse": { + "Package": "tidyverse", + "Version": "2.0.0", + "Source": "Repository" + }, + "timechange": { + "Package": "timechange", + "Version": "0.3.0", + "Source": "Repository" + }, + "tinytex": { + "Package": "tinytex", + "Version": "0.50", + "Source": "Repository" + }, + "tools": { + "Package": "tools", + "Version": "4.3.3", + "Source": "R" + }, + "tweenr": { + "Package": "tweenr", + "Version": "2.0.3", + "Source": "Repository" + }, + "tximport": { + "Package": "tximport", + "Version": "1.30.0", + "Source": "Bioconductor", + "Requirements": [ + "methods", + "stats", + "utils" + ], + "Hash": "6e9621b0f1bf9398255f32c7000a7e16" + }, + "tzdb": { + "Package": "tzdb", + "Version": "0.4.0", + "Source": "Repository" + }, + "utf8": { + "Package": "utf8", + "Version": "1.2.4", + "Source": "Repository" + }, + "utils": { + "Package": "utils", + "Version": "4.3.3", + "Source": "R" + }, + "uuid": { + "Package": "uuid", + "Version": "1.2-0", + "Source": "Repository" + }, + "vctrs": { + "Package": "vctrs", + "Version": "0.6.5", + "Source": "Repository" + }, + "viridisLite": { + "Package": "viridisLite", + "Version": "0.4.2", + "Source": "Repository" + }, + "vroom": { + "Package": "vroom", + "Version": "1.6.5", + "Source": "Repository" + }, + "withr": { + "Package": "withr", + "Version": "3.0.0", + "Source": "Repository" + }, + "xfun": { + "Package": "xfun", + "Version": "0.43", + "Source": "Repository" + }, + "xml2": { + "Package": "xml2", + "Version": "1.3.6", + "Source": "Repository" + }, + "yaml": { + "Package": "yaml", + "Version": "2.3.8", + "Source": "Repository" + }, + "zlibbioc": { + "Package": "zlibbioc", + "Version": "1.48.2", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Hash": "2344be62c2da4d9e9942b5d8db346e59" + } + } +} diff --git a/docker/renv_seurat.lock b/docker/renv_seurat.lock new file mode 100644 index 00000000..63e64fcb --- /dev/null +++ b/docker/renv_seurat.lock @@ -0,0 +1,1777 @@ +{ + "R": { + "Version": "4.3.3", + "Repositories": [ + { + "Name": "BioCsoft", + "URL": "https://bioconductor.org/packages/3.18/bioc" + }, + { + "Name": "BioCann", + "URL": "https://bioconductor.org/packages/3.18/data/annotation" + }, + { + "Name": "BioCexp", + "URL": "https://bioconductor.org/packages/3.18/data/experiment" + }, + { + "Name": "BioCworkflows", + "URL": "https://bioconductor.org/packages/3.18/workflows" + }, + { + "Name": "BioCbooks", + "URL": "https://bioconductor.org/packages/3.18/books" + }, + { + "Name": "CRAN", + "URL": "https://p3m.dev/cran/latest" + } + ] + }, + "Bioconductor": { + "Version": "3.18" + }, + "Packages": { + "BH": { + "Package": "BH", + "Version": "1.84.0-0", + "Source": "Repository" + }, + "Biobase": { + "Package": "Biobase", + "Version": "2.62.0", + "Source": "Bioconductor", + "Requirements": [ + "BiocGenerics", + "R", + "methods", + "utils" + ], + "Hash": "38252a34e82d3ff6bb46b4e2252d2dce" + }, + "BiocGenerics": { + "Package": "BiocGenerics", + "Version": "0.48.1", + "Source": "Bioconductor", + "Requirements": [ + "R", + "graphics", + "methods", + "stats", + "utils" + ], + "Hash": "e34278c65d7dffcc08f737bf0944ca9a" + }, + "BiocManager": { + "Package": "BiocManager", + "Version": "1.30.22", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "utils" + ], + "Hash": "d57e43105a1aa9cb54fdb4629725acb1" + }, + "BiocNeighbors": { + "Package": "BiocNeighbors", + "Version": "1.20.2", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "BiocParallel", + "Matrix", + "Rcpp", + "RcppHNSW", + "S4Vectors", + "methods", + "stats" + ], + "Hash": "c5c8ade5852fd3b25c66ec28873d00f1" + }, + "BiocParallel": { + "Package": "BiocParallel", + "Version": "1.36.0", + "Source": "Bioconductor", + "Requirements": [ + "BH", + "R", + "codetools", + "cpp11", + "futile.logger", + "methods", + "parallel", + "snow", + "stats", + "utils" + ], + "Hash": "6d1689ee8b65614ba6ef4012a67b663a" + }, + "BiocVersion": { + "Package": "BiocVersion", + "Version": "3.18.1", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "R" + ], + "Hash": "2ecaed86684f5fae76ed5530f9d29c4a" + }, + "DBI": { + "Package": "DBI", + "Version": "1.2.2", + "Source": "Repository" + }, + "DelayedArray": { + "Package": "DelayedArray", + "Version": "0.28.0", + "Source": "Bioconductor", + "Requirements": [ + "BiocGenerics", + "IRanges", + "Matrix", + "MatrixGenerics", + "R", + "S4Arrays", + "S4Vectors", + "SparseArray", + "methods", + "stats", + "stats4" + ], + "Hash": "0e5c84e543a3d04ce64c6f60ed46d7eb" + }, + "DelayedMatrixStats": { + "Package": "DelayedMatrixStats", + "Version": "1.24.0", + "Source": "Bioconductor", + "Requirements": [ + "DelayedArray", + "IRanges", + "Matrix", + "MatrixGenerics", + "S4Vectors", + "methods", + "sparseMatrixStats" + ], + "Hash": "71c2d178d33f9d91999f67dc2d53b747" + }, + "DropletUtils": { + "Package": "DropletUtils", + "Version": "1.22.0", + "Source": "Bioconductor", + "Requirements": [ + "BH", + "BiocGenerics", + "BiocParallel", + "DelayedArray", + "DelayedMatrixStats", + "GenomicRanges", + "HDF5Array", + "IRanges", + "Matrix", + "R.utils", + "Rcpp", + "Rhdf5lib", + "S4Vectors", + "SingleCellExperiment", + "SummarizedExperiment", + "beachmat", + "dqrng", + "edgeR", + "methods", + "rhdf5", + "scuttle", + "stats", + "utils" + ], + "Hash": "be3893d30c97591f1d3ec6f053830c3a" + }, + "FNN": { + "Package": "FNN", + "Version": "1.1.4", + "Source": "Repository" + }, + "GenomeInfoDb": { + "Package": "GenomeInfoDb", + "Version": "1.38.8", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "BiocGenerics", + "GenomeInfoDbData", + "IRanges", + "R", + "RCurl", + "S4Vectors", + "methods", + "stats", + "stats4", + "utils" + ], + "Hash": "155053909d2831bfac154a1118151d6b" + }, + "GenomeInfoDbData": { + "Package": "GenomeInfoDbData", + "Version": "1.2.11", + "Source": "Bioconductor", + "Requirements": [ + "R" + ], + "Hash": "10f32956181d1d46bd8402c93ac193e8" + }, + "GenomicRanges": { + "Package": "GenomicRanges", + "Version": "1.54.1", + "Source": "Bioconductor", + "Requirements": [ + "BiocGenerics", + "GenomeInfoDb", + "IRanges", + "R", + "S4Vectors", + "XVector", + "methods", + "stats", + "stats4", + "utils" + ], + "Hash": "7e0c1399af35369312d9c399454374e8" + }, + "HDF5Array": { + "Package": "HDF5Array", + "Version": "1.30.1", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "BiocGenerics", + "DelayedArray", + "IRanges", + "Matrix", + "R", + "Rhdf5lib", + "S4Arrays", + "S4Vectors", + "methods", + "rhdf5", + "rhdf5filters", + "stats", + "tools", + "utils" + ], + "Hash": "9b8deb4fd34fa439c16c829457d1968f" + }, + "IRanges": { + "Package": "IRanges", + "Version": "2.36.0", + "Source": "Bioconductor", + "Requirements": [ + "BiocGenerics", + "R", + "S4Vectors", + "methods", + "stats", + "stats4", + "utils" + ], + "Hash": "f98500eeb93e8a66ad65be955a848595" + }, + "KernSmooth": { + "Package": "KernSmooth", + "Version": "2.23-22", + "Source": "Repository" + }, + "MASS": { + "Package": "MASS", + "Version": "7.3-60.0.1", + "Source": "Repository" + }, + "Matrix": { + "Package": "Matrix", + "Version": "1.6-5", + "Source": "Repository" + }, + "MatrixGenerics": { + "Package": "MatrixGenerics", + "Version": "1.14.0", + "Source": "Bioconductor", + "Requirements": [ + "matrixStats", + "methods" + ], + "Hash": "088cd2077b5619fcb7b373b1a45174e7" + }, + "R.methodsS3": { + "Package": "R.methodsS3", + "Version": "1.8.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "utils" + ], + "Hash": "278c286fd6e9e75d0c2e8f731ea445c8" + }, + "R.oo": { + "Package": "R.oo", + "Version": "1.26.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "R.methodsS3", + "methods", + "utils" + ], + "Hash": "4fed809e53ddb5407b3da3d0f572e591" + }, + "R.utils": { + "Package": "R.utils", + "Version": "2.12.3", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "R.methodsS3", + "R.oo", + "methods", + "tools", + "utils" + ], + "Hash": "3dc2829b790254bfba21e60965787651" + }, + "R6": { + "Package": "R6", + "Version": "2.5.1", + "Source": "Repository" + }, + "RANN": { + "Package": "RANN", + "Version": "2.6.1", + "Source": "Repository" + }, + "RColorBrewer": { + "Package": "RColorBrewer", + "Version": "1.1-3", + "Source": "Repository" + }, + "RCurl": { + "Package": "RCurl", + "Version": "1.98-1.14", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "bitops", + "methods" + ], + "Hash": "47f648d288079d0c696804ad4e55197e" + }, + "ROCR": { + "Package": "ROCR", + "Version": "1.0-11", + "Source": "Repository" + }, + "RSpectra": { + "Package": "RSpectra", + "Version": "0.16-1", + "Source": "Repository" + }, + "Rcpp": { + "Package": "Rcpp", + "Version": "1.0.12", + "Source": "Repository" + }, + "RcppAnnoy": { + "Package": "RcppAnnoy", + "Version": "0.0.22", + "Source": "Repository" + }, + "RcppArmadillo": { + "Package": "RcppArmadillo", + "Version": "0.12.8.2.1", + "Source": "Repository" + }, + "RcppEigen": { + "Package": "RcppEigen", + "Version": "0.3.4.0.0", + "Source": "Repository" + }, + "RcppHNSW": { + "Package": "RcppHNSW", + "Version": "0.6.0", + "Source": "Repository" + }, + "RcppProgress": { + "Package": "RcppProgress", + "Version": "0.4.2", + "Source": "Repository" + }, + "RcppTOML": { + "Package": "RcppTOML", + "Version": "0.2.2", + "Source": "Repository" + }, + "Rhdf5lib": { + "Package": "Rhdf5lib", + "Version": "1.24.2", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "R" + ], + "Hash": "3cf103db29d75af0221d71946509a30c" + }, + "Rtsne": { + "Package": "Rtsne", + "Version": "0.17", + "Source": "Repository" + }, + "S4Arrays": { + "Package": "S4Arrays", + "Version": "1.2.1", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "BiocGenerics", + "IRanges", + "Matrix", + "R", + "S4Vectors", + "abind", + "crayon", + "methods", + "stats" + ], + "Hash": "3213a9826adb8f48e51af1e7b30fa568" + }, + "S4Vectors": { + "Package": "S4Vectors", + "Version": "0.40.2", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "BiocGenerics", + "R", + "methods", + "stats", + "stats4", + "utils" + ], + "Hash": "1716e201f81ced0f456dd5ec85fe20f8" + }, + "Seurat": { + "Package": "Seurat", + "Version": "5.0.3", + "Source": "Repository" + }, + "SeuratObject": { + "Package": "SeuratObject", + "Version": "5.0.1", + "Source": "Repository" + }, + "SingleCellExperiment": { + "Package": "SingleCellExperiment", + "Version": "1.24.0", + "Source": "Bioconductor", + "Requirements": [ + "BiocGenerics", + "DelayedArray", + "GenomicRanges", + "S4Vectors", + "SummarizedExperiment", + "methods", + "stats", + "utils" + ], + "Hash": "e21b3571ce76eb4dfe6bf7900960aa6a" + }, + "SparseArray": { + "Package": "SparseArray", + "Version": "1.2.4", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "BiocGenerics", + "IRanges", + "Matrix", + "MatrixGenerics", + "R", + "S4Arrays", + "S4Vectors", + "XVector", + "matrixStats", + "methods", + "stats" + ], + "Hash": "391092e7b81373ab624bd6471cebccd4" + }, + "SummarizedExperiment": { + "Package": "SummarizedExperiment", + "Version": "1.32.0", + "Source": "Bioconductor", + "Requirements": [ + "Biobase", + "BiocGenerics", + "DelayedArray", + "GenomeInfoDb", + "GenomicRanges", + "IRanges", + "Matrix", + "MatrixGenerics", + "R", + "S4Arrays", + "S4Vectors", + "methods", + "stats", + "tools", + "utils" + ], + "Hash": "caee529bf9710ff6fe1776612fcaa266" + }, + "XVector": { + "Package": "XVector", + "Version": "0.42.0", + "Source": "Bioconductor", + "Requirements": [ + "BiocGenerics", + "IRanges", + "R", + "S4Vectors", + "methods", + "tools", + "utils", + "zlibbioc" + ], + "Hash": "65c0b6bca03f88758f86ef0aa18c4873" + }, + "abind": { + "Package": "abind", + "Version": "1.4-5", + "Source": "Repository" + }, + "askpass": { + "Package": "askpass", + "Version": "1.2.0", + "Source": "Repository" + }, + "backports": { + "Package": "backports", + "Version": "1.4.1", + "Source": "Repository" + }, + "base64enc": { + "Package": "base64enc", + "Version": "0.1-3", + "Source": "Repository" + }, + "beachmat": { + "Package": "beachmat", + "Version": "2.18.1", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "BiocGenerics", + "DelayedArray", + "Matrix", + "Rcpp", + "SparseArray", + "methods" + ], + "Hash": "c1c423ca7149d9e7f55d1e609342c2bd" + }, + "bit": { + "Package": "bit", + "Version": "4.0.5", + "Source": "Repository" + }, + "bit64": { + "Package": "bit64", + "Version": "4.0.5", + "Source": "Repository" + }, + "bitops": { + "Package": "bitops", + "Version": "1.0-7", + "Source": "Repository" + }, + "blob": { + "Package": "blob", + "Version": "1.2.4", + "Source": "Repository" + }, + "bluster": { + "Package": "bluster", + "Version": "1.12.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "BiocNeighbors", + "BiocParallel", + "Matrix", + "Rcpp", + "S4Vectors", + "cluster", + "igraph", + "methods", + "stats", + "utils" + ], + "Hash": "fca0d5ffad6380f13cad4d7855107aef" + }, + "broom": { + "Package": "broom", + "Version": "1.0.5", + "Source": "Repository" + }, + "bslib": { + "Package": "bslib", + "Version": "0.7.0", + "Source": "Repository" + }, + "caTools": { + "Package": "caTools", + "Version": "1.18.2", + "Source": "Repository" + }, + "cachem": { + "Package": "cachem", + "Version": "1.0.8", + "Source": "Repository" + }, + "callr": { + "Package": "callr", + "Version": "3.7.6", + "Source": "Repository" + }, + "cellranger": { + "Package": "cellranger", + "Version": "1.1.0", + "Source": "Repository" + }, + "cli": { + "Package": "cli", + "Version": "3.6.2", + "Source": "Repository" + }, + "clipr": { + "Package": "clipr", + "Version": "0.8.0", + "Source": "Repository" + }, + "cluster": { + "Package": "cluster", + "Version": "2.1.6", + "Source": "Repository" + }, + "codetools": { + "Package": "codetools", + "Version": "0.2-20", + "Source": "Repository" + }, + "colorspace": { + "Package": "colorspace", + "Version": "2.1-0", + "Source": "Repository" + }, + "commonmark": { + "Package": "commonmark", + "Version": "1.9.1", + "Source": "Repository" + }, + "conflicted": { + "Package": "conflicted", + "Version": "1.2.0", + "Source": "Repository" + }, + "cowplot": { + "Package": "cowplot", + "Version": "1.1.3", + "Source": "Repository" + }, + "cpp11": { + "Package": "cpp11", + "Version": "0.4.7", + "Source": "Repository" + }, + "crayon": { + "Package": "crayon", + "Version": "1.5.2", + "Source": "Repository" + }, + "crosstalk": { + "Package": "crosstalk", + "Version": "1.2.1", + "Source": "Repository" + }, + "curl": { + "Package": "curl", + "Version": "5.2.1", + "Source": "Repository" + }, + "data.table": { + "Package": "data.table", + "Version": "1.15.4", + "Source": "Repository" + }, + "dbplyr": { + "Package": "dbplyr", + "Version": "2.5.0", + "Source": "Repository" + }, + "deldir": { + "Package": "deldir", + "Version": "2.0-4", + "Source": "Repository" + }, + "digest": { + "Package": "digest", + "Version": "0.6.35", + "Source": "Repository" + }, + "dotCall64": { + "Package": "dotCall64", + "Version": "1.1-1", + "Source": "Repository" + }, + "dplyr": { + "Package": "dplyr", + "Version": "1.1.4", + "Source": "Repository" + }, + "dqrng": { + "Package": "dqrng", + "Version": "0.3.2", + "Source": "Repository" + }, + "dtplyr": { + "Package": "dtplyr", + "Version": "1.3.1", + "Source": "Repository" + }, + "edgeR": { + "Package": "edgeR", + "Version": "4.0.16", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "R", + "Rcpp", + "graphics", + "limma", + "locfit", + "methods", + "stats", + "utils" + ], + "Hash": "a0405c7890708dcb53809d46758800f4" + }, + "ellipsis": { + "Package": "ellipsis", + "Version": "0.3.2", + "Source": "Repository" + }, + "evaluate": { + "Package": "evaluate", + "Version": "0.23", + "Source": "Repository" + }, + "fansi": { + "Package": "fansi", + "Version": "1.0.6", + "Source": "Repository" + }, + "farver": { + "Package": "farver", + "Version": "2.1.1", + "Source": "Repository" + }, + "fastDummies": { + "Package": "fastDummies", + "Version": "1.7.3", + "Source": "Repository" + }, + "fastmap": { + "Package": "fastmap", + "Version": "1.1.1", + "Source": "Repository" + }, + "fishpond": { + "Package": "fishpond", + "Version": "2.8.0", + "Source": "Bioconductor", + "Requirements": [ + "GenomicRanges", + "IRanges", + "Matrix", + "S4Vectors", + "SingleCellExperiment", + "SummarizedExperiment", + "abind", + "graphics", + "gtools", + "jsonlite", + "matrixStats", + "methods", + "qvalue", + "stats", + "svMisc", + "utils" + ], + "Hash": "60ebe3366ccb6c1a11a99682f56f2a2f" + }, + "fitdistrplus": { + "Package": "fitdistrplus", + "Version": "1.1-11", + "Source": "Repository" + }, + "flexmix": { + "Package": "flexmix", + "Version": "2.3-19", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "grDevices", + "graphics", + "grid", + "lattice", + "methods", + "modeltools", + "nnet", + "stats", + "stats4", + "utils" + ], + "Hash": "0cb3c4b251c2d3fd5923d3e7e6021ee2" + }, + "fontawesome": { + "Package": "fontawesome", + "Version": "0.5.2", + "Source": "Repository" + }, + "forcats": { + "Package": "forcats", + "Version": "1.0.0", + "Source": "Repository" + }, + "formatR": { + "Package": "formatR", + "Version": "1.14", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R" + ], + "Hash": "63cb26d12517c7863f5abb006c5e0f25" + }, + "fs": { + "Package": "fs", + "Version": "1.6.3", + "Source": "Repository" + }, + "futile.logger": { + "Package": "futile.logger", + "Version": "1.4.3", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "futile.options", + "lambda.r", + "utils" + ], + "Hash": "99f0ace8c05ec7d3683d27083c4f1e7e" + }, + "futile.options": { + "Package": "futile.options", + "Version": "1.0.1", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R" + ], + "Hash": "0d9bf02413ddc2bbe8da9ce369dcdd2b" + }, + "future": { + "Package": "future", + "Version": "1.33.2", + "Source": "Repository" + }, + "future.apply": { + "Package": "future.apply", + "Version": "1.11.2", + "Source": "Repository" + }, + "gargle": { + "Package": "gargle", + "Version": "1.5.2", + "Source": "Repository" + }, + "generics": { + "Package": "generics", + "Version": "0.1.3", + "Source": "Repository" + }, + "getopt": { + "Package": "getopt", + "Version": "1.20.4", + "Source": "Repository" + }, + "ggplot2": { + "Package": "ggplot2", + "Version": "3.5.0", + "Source": "Repository" + }, + "ggrepel": { + "Package": "ggrepel", + "Version": "0.9.5", + "Source": "Repository" + }, + "ggridges": { + "Package": "ggridges", + "Version": "0.5.6", + "Source": "Repository" + }, + "globals": { + "Package": "globals", + "Version": "0.16.3", + "Source": "Repository" + }, + "glue": { + "Package": "glue", + "Version": "1.7.0", + "Source": "Repository" + }, + "goftest": { + "Package": "goftest", + "Version": "1.2-3", + "Source": "Repository" + }, + "googledrive": { + "Package": "googledrive", + "Version": "2.1.1", + "Source": "Repository" + }, + "googlesheets4": { + "Package": "googlesheets4", + "Version": "1.1.1", + "Source": "Repository" + }, + "gplots": { + "Package": "gplots", + "Version": "3.1.3.1", + "Source": "Repository" + }, + "grDevices": { + "Package": "grDevices", + "Version": "4.3.3", + "Source": "R" + }, + "graphics": { + "Package": "graphics", + "Version": "4.3.3", + "Source": "R" + }, + "grid": { + "Package": "grid", + "Version": "4.3.3", + "Source": "R" + }, + "gridExtra": { + "Package": "gridExtra", + "Version": "2.3", + "Source": "Repository" + }, + "gtable": { + "Package": "gtable", + "Version": "0.3.5", + "Source": "Repository" + }, + "gtools": { + "Package": "gtools", + "Version": "3.9.5", + "Source": "Repository" + }, + "haven": { + "Package": "haven", + "Version": "2.5.4", + "Source": "Repository" + }, + "here": { + "Package": "here", + "Version": "1.0.1", + "Source": "Repository" + }, + "highr": { + "Package": "highr", + "Version": "0.10", + "Source": "Repository" + }, + "hms": { + "Package": "hms", + "Version": "1.1.3", + "Source": "Repository" + }, + "htmltools": { + "Package": "htmltools", + "Version": "0.5.8.1", + "Source": "Repository" + }, + "htmlwidgets": { + "Package": "htmlwidgets", + "Version": "1.6.4", + "Source": "Repository" + }, + "httpuv": { + "Package": "httpuv", + "Version": "1.6.15", + "Source": "Repository" + }, + "httr": { + "Package": "httr", + "Version": "1.4.7", + "Source": "Repository" + }, + "ica": { + "Package": "ica", + "Version": "1.0-3", + "Source": "Repository" + }, + "ids": { + "Package": "ids", + "Version": "1.0.1", + "Source": "Repository" + }, + "igraph": { + "Package": "igraph", + "Version": "2.0.3", + "Source": "Repository" + }, + "irlba": { + "Package": "irlba", + "Version": "2.3.5.1", + "Source": "Repository" + }, + "isoband": { + "Package": "isoband", + "Version": "0.2.7", + "Source": "Repository" + }, + "jquerylib": { + "Package": "jquerylib", + "Version": "0.1.4", + "Source": "Repository" + }, + "jsonlite": { + "Package": "jsonlite", + "Version": "1.8.8", + "Source": "Repository" + }, + "knitr": { + "Package": "knitr", + "Version": "1.46", + "Source": "Repository" + }, + "labeling": { + "Package": "labeling", + "Version": "0.4.3", + "Source": "Repository" + }, + "lambda.r": { + "Package": "lambda.r", + "Version": "1.2.4", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "formatR" + ], + "Hash": "b1e925c4b9ffeb901bacf812cbe9a6ad" + }, + "later": { + "Package": "later", + "Version": "1.3.2", + "Source": "Repository" + }, + "lattice": { + "Package": "lattice", + "Version": "0.22-6", + "Source": "Repository" + }, + "lazyeval": { + "Package": "lazyeval", + "Version": "0.2.2", + "Source": "Repository" + }, + "leiden": { + "Package": "leiden", + "Version": "0.4.3.1", + "Source": "Repository" + }, + "lifecycle": { + "Package": "lifecycle", + "Version": "1.0.4", + "Source": "Repository" + }, + "limma": { + "Package": "limma", + "Version": "3.58.1", + "Source": "Bioconductor", + "Requirements": [ + "R", + "grDevices", + "graphics", + "methods", + "statmod", + "stats", + "utils" + ], + "Hash": "74c3b64358e0be7edc3ecd130816dd3f" + }, + "listenv": { + "Package": "listenv", + "Version": "0.9.1", + "Source": "Repository" + }, + "lmtest": { + "Package": "lmtest", + "Version": "0.9-40", + "Source": "Repository" + }, + "locfit": { + "Package": "locfit", + "Version": "1.5-9.9", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "lattice" + ], + "Hash": "3885127e04b35dafded049075057ad83" + }, + "lubridate": { + "Package": "lubridate", + "Version": "1.9.3", + "Source": "Repository" + }, + "magrittr": { + "Package": "magrittr", + "Version": "2.0.3", + "Source": "Repository" + }, + "matrixStats": { + "Package": "matrixStats", + "Version": "1.3.0", + "Source": "Repository" + }, + "memoise": { + "Package": "memoise", + "Version": "2.0.1", + "Source": "Repository" + }, + "methods": { + "Package": "methods", + "Version": "4.3.3", + "Source": "R" + }, + "mgcv": { + "Package": "mgcv", + "Version": "1.9-1", + "Source": "Repository" + }, + "miQC": { + "Package": "miQC", + "Version": "1.10.0", + "Source": "Bioconductor", + "Requirements": [ + "R", + "SingleCellExperiment", + "flexmix", + "ggplot2", + "splines" + ], + "Hash": "5d3660451d88509307ce0b0e48748109" + }, + "mime": { + "Package": "mime", + "Version": "0.12", + "Source": "Repository" + }, + "miniUI": { + "Package": "miniUI", + "Version": "0.1.1.1", + "Source": "Repository" + }, + "modelr": { + "Package": "modelr", + "Version": "0.1.11", + "Source": "Repository" + }, + "modeltools": { + "Package": "modeltools", + "Version": "0.2-23", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "methods", + "stats", + "stats4" + ], + "Hash": "f5a957c02222589bdf625a67be68b2a9" + }, + "munsell": { + "Package": "munsell", + "Version": "0.5.1", + "Source": "Repository" + }, + "nlme": { + "Package": "nlme", + "Version": "3.1-164", + "Source": "Repository" + }, + "nnet": { + "Package": "nnet", + "Version": "7.3-19", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "stats", + "utils" + ], + "Hash": "2c797b46eea7fb58ede195bc0b1f1138" + }, + "openssl": { + "Package": "openssl", + "Version": "2.1.2", + "Source": "Repository" + }, + "optparse": { + "Package": "optparse", + "Version": "1.7.5", + "Source": "Repository" + }, + "parallel": { + "Package": "parallel", + "Version": "4.3.3", + "Source": "R" + }, + "parallelly": { + "Package": "parallelly", + "Version": "1.37.1", + "Source": "Repository" + }, + "patchwork": { + "Package": "patchwork", + "Version": "1.2.0", + "Source": "Repository" + }, + "pbapply": { + "Package": "pbapply", + "Version": "1.7-2", + "Source": "Repository" + }, + "pillar": { + "Package": "pillar", + "Version": "1.9.0", + "Source": "Repository" + }, + "pkgconfig": { + "Package": "pkgconfig", + "Version": "2.0.3", + "Source": "Repository" + }, + "plotly": { + "Package": "plotly", + "Version": "4.10.4", + "Source": "Repository" + }, + "plyr": { + "Package": "plyr", + "Version": "1.8.9", + "Source": "Repository" + }, + "png": { + "Package": "png", + "Version": "0.1-8", + "Source": "Repository" + }, + "polyclip": { + "Package": "polyclip", + "Version": "1.10-6", + "Source": "Repository" + }, + "prettyunits": { + "Package": "prettyunits", + "Version": "1.2.0", + "Source": "Repository" + }, + "processx": { + "Package": "processx", + "Version": "3.8.4", + "Source": "Repository" + }, + "progress": { + "Package": "progress", + "Version": "1.2.3", + "Source": "Repository" + }, + "progressr": { + "Package": "progressr", + "Version": "0.14.0", + "Source": "Repository" + }, + "promises": { + "Package": "promises", + "Version": "1.3.0", + "Source": "Repository" + }, + "ps": { + "Package": "ps", + "Version": "1.7.6", + "Source": "Repository" + }, + "purrr": { + "Package": "purrr", + "Version": "1.0.2", + "Source": "Repository" + }, + "qvalue": { + "Package": "qvalue", + "Version": "2.34.0", + "Source": "Bioconductor", + "Requirements": [ + "R", + "ggplot2", + "grid", + "reshape2", + "splines" + ], + "Hash": "76fc42834c44b69e4021f6ade524d299" + }, + "ragg": { + "Package": "ragg", + "Version": "1.3.0", + "Source": "Repository" + }, + "rappdirs": { + "Package": "rappdirs", + "Version": "0.3.3", + "Source": "Repository" + }, + "readr": { + "Package": "readr", + "Version": "2.1.5", + "Source": "Repository" + }, + "readxl": { + "Package": "readxl", + "Version": "1.4.3", + "Source": "Repository" + }, + "rematch": { + "Package": "rematch", + "Version": "2.0.0", + "Source": "Repository" + }, + "rematch2": { + "Package": "rematch2", + "Version": "2.1.2", + "Source": "Repository" + }, + "renv": { + "Package": "renv", + "Version": "1.0.7", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "utils" + ], + "Hash": "397b7b2a265bc5a7a06852524dabae20" + }, + "reprex": { + "Package": "reprex", + "Version": "2.1.0", + "Source": "Repository" + }, + "reshape2": { + "Package": "reshape2", + "Version": "1.4.4", + "Source": "Repository" + }, + "reticulate": { + "Package": "reticulate", + "Version": "1.36.1", + "Source": "Repository" + }, + "rhdf5": { + "Package": "rhdf5", + "Version": "2.46.1", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "R", + "Rhdf5lib", + "S4Vectors", + "methods", + "rhdf5filters" + ], + "Hash": "b0a244022c3427cd8213c33804c6b5de" + }, + "rhdf5filters": { + "Package": "rhdf5filters", + "Version": "1.14.1", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "Rhdf5lib" + ], + "Hash": "d27a2f6a89def6388fad5b0aae026220" + }, + "rlang": { + "Package": "rlang", + "Version": "1.1.3", + "Source": "Repository" + }, + "rmarkdown": { + "Package": "rmarkdown", + "Version": "2.26", + "Source": "Repository" + }, + "rprojroot": { + "Package": "rprojroot", + "Version": "2.0.4", + "Source": "Repository" + }, + "rstudioapi": { + "Package": "rstudioapi", + "Version": "0.16.0", + "Source": "Repository" + }, + "rvest": { + "Package": "rvest", + "Version": "1.0.4", + "Source": "Repository" + }, + "sass": { + "Package": "sass", + "Version": "0.4.9", + "Source": "Repository" + }, + "scales": { + "Package": "scales", + "Version": "1.3.0", + "Source": "Repository" + }, + "scattermore": { + "Package": "scattermore", + "Version": "1.2", + "Source": "Repository" + }, + "sctransform": { + "Package": "sctransform", + "Version": "0.4.1", + "Source": "Repository" + }, + "scuttle": { + "Package": "scuttle", + "Version": "1.12.0", + "Source": "Bioconductor", + "Requirements": [ + "BiocGenerics", + "BiocParallel", + "DelayedArray", + "DelayedMatrixStats", + "GenomicRanges", + "Matrix", + "Rcpp", + "S4Vectors", + "SingleCellExperiment", + "SummarizedExperiment", + "beachmat", + "methods", + "stats", + "utils" + ], + "Hash": "1412c4b6dfd8de528e1101e493e66a02" + }, + "selectr": { + "Package": "selectr", + "Version": "0.4-2", + "Source": "Repository" + }, + "shiny": { + "Package": "shiny", + "Version": "1.8.1.1", + "Source": "Repository" + }, + "sitmo": { + "Package": "sitmo", + "Version": "2.0.2", + "Source": "Repository" + }, + "snow": { + "Package": "snow", + "Version": "0.4-4", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "utils" + ], + "Hash": "40b74690debd20c57d93d8c246b305d4" + }, + "sourcetools": { + "Package": "sourcetools", + "Version": "0.1.7-1", + "Source": "Repository" + }, + "sp": { + "Package": "sp", + "Version": "2.1-3", + "Source": "Repository" + }, + "spam": { + "Package": "spam", + "Version": "2.10-0", + "Source": "Repository" + }, + "sparseMatrixStats": { + "Package": "sparseMatrixStats", + "Version": "1.14.0", + "Source": "Bioconductor", + "Requirements": [ + "Matrix", + "MatrixGenerics", + "Rcpp", + "matrixStats", + "methods" + ], + "Hash": "49383d0f6c6152ff7cb594f254c23cc8" + }, + "spatstat.data": { + "Package": "spatstat.data", + "Version": "3.0-4", + "Source": "Repository" + }, + "spatstat.explore": { + "Package": "spatstat.explore", + "Version": "3.2-7", + "Source": "Repository" + }, + "spatstat.geom": { + "Package": "spatstat.geom", + "Version": "3.2-9", + "Source": "Repository" + }, + "spatstat.random": { + "Package": "spatstat.random", + "Version": "3.2-3", + "Source": "Repository" + }, + "spatstat.sparse": { + "Package": "spatstat.sparse", + "Version": "3.0-3", + "Source": "Repository" + }, + "spatstat.utils": { + "Package": "spatstat.utils", + "Version": "3.0-4", + "Source": "Repository" + }, + "splines": { + "Package": "splines", + "Version": "4.3.3", + "Source": "R" + }, + "statmod": { + "Package": "statmod", + "Version": "1.5.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "graphics", + "stats" + ], + "Hash": "26e158d12052c279bdd4ba858b80fb1f" + }, + "stats": { + "Package": "stats", + "Version": "4.3.3", + "Source": "R" + }, + "stringi": { + "Package": "stringi", + "Version": "1.8.3", + "Source": "Repository" + }, + "stringr": { + "Package": "stringr", + "Version": "1.5.1", + "Source": "Repository" + }, + "survival": { + "Package": "survival", + "Version": "3.5-8", + "Source": "Repository" + }, + "svMisc": { + "Package": "svMisc", + "Version": "1.2.3", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "methods", + "stats", + "tools", + "utils" + ], + "Hash": "b13f5680860f67c32ccb006ad38f24f4" + }, + "sys": { + "Package": "sys", + "Version": "3.4.2", + "Source": "Repository" + }, + "systemfonts": { + "Package": "systemfonts", + "Version": "1.0.6", + "Source": "Repository" + }, + "tensor": { + "Package": "tensor", + "Version": "1.5", + "Source": "Repository" + }, + "textshaping": { + "Package": "textshaping", + "Version": "0.3.7", + "Source": "Repository" + }, + "tibble": { + "Package": "tibble", + "Version": "3.2.1", + "Source": "Repository" + }, + "tidyr": { + "Package": "tidyr", + "Version": "1.3.1", + "Source": "Repository" + }, + "tidyselect": { + "Package": "tidyselect", + "Version": "1.2.1", + "Source": "Repository" + }, + "tidyverse": { + "Package": "tidyverse", + "Version": "2.0.0", + "Source": "Repository" + }, + "timechange": { + "Package": "timechange", + "Version": "0.3.0", + "Source": "Repository" + }, + "tinytex": { + "Package": "tinytex", + "Version": "0.50", + "Source": "Repository" + }, + "tools": { + "Package": "tools", + "Version": "4.3.3", + "Source": "R" + }, + "tximport": { + "Package": "tximport", + "Version": "1.30.0", + "Source": "Bioconductor", + "Requirements": [ + "methods", + "stats", + "utils" + ], + "Hash": "6e9621b0f1bf9398255f32c7000a7e16" + }, + "tzdb": { + "Package": "tzdb", + "Version": "0.4.0", + "Source": "Repository" + }, + "utf8": { + "Package": "utf8", + "Version": "1.2.4", + "Source": "Repository" + }, + "utils": { + "Package": "utils", + "Version": "4.3.3", + "Source": "R" + }, + "uuid": { + "Package": "uuid", + "Version": "1.2-0", + "Source": "Repository" + }, + "uwot": { + "Package": "uwot", + "Version": "0.2.2", + "Source": "Repository" + }, + "vctrs": { + "Package": "vctrs", + "Version": "0.6.5", + "Source": "Repository" + }, + "viridisLite": { + "Package": "viridisLite", + "Version": "0.4.2", + "Source": "Repository" + }, + "vroom": { + "Package": "vroom", + "Version": "1.6.5", + "Source": "Repository" + }, + "withr": { + "Package": "withr", + "Version": "3.0.0", + "Source": "Repository" + }, + "xfun": { + "Package": "xfun", + "Version": "0.43", + "Source": "Repository" + }, + "xml2": { + "Package": "xml2", + "Version": "1.3.6", + "Source": "Repository" + }, + "xtable": { + "Package": "xtable", + "Version": "1.8-4", + "Source": "Repository" + }, + "yaml": { + "Package": "yaml", + "Version": "2.3.8", + "Source": "Repository" + }, + "zlibbioc": { + "Package": "zlibbioc", + "Version": "1.48.2", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Hash": "2344be62c2da4d9e9942b5d8db346e59" + }, + "zoo": { + "Package": "zoo", + "Version": "1.8-12", + "Source": "Repository" + } + } +} diff --git a/docker/renv_slim.lock b/docker/renv_slim.lock new file mode 100644 index 00000000..f17b18b6 --- /dev/null +++ b/docker/renv_slim.lock @@ -0,0 +1,1532 @@ +{ + "R": { + "Version": "4.3.3", + "Repositories": [ + { + "Name": "BioCsoft", + "URL": "https://bioconductor.org/packages/3.18/bioc" + }, + { + "Name": "BioCann", + "URL": "https://bioconductor.org/packages/3.18/data/annotation" + }, + { + "Name": "BioCexp", + "URL": "https://bioconductor.org/packages/3.18/data/experiment" + }, + { + "Name": "BioCworkflows", + "URL": "https://bioconductor.org/packages/3.18/workflows" + }, + { + "Name": "BioCbooks", + "URL": "https://bioconductor.org/packages/3.18/books" + }, + { + "Name": "CRAN", + "URL": "https://p3m.dev/cran/latest" + } + ] + }, + "Bioconductor": { + "Version": "3.18" + }, + "Packages": { + "BH": { + "Package": "BH", + "Version": "1.84.0-0", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "a8235afbcd6316e6e91433ea47661013" + }, + "Biobase": { + "Package": "Biobase", + "Version": "2.62.0", + "Source": "Bioconductor", + "Requirements": [ + "BiocGenerics", + "R", + "methods", + "utils" + ], + "Hash": "38252a34e82d3ff6bb46b4e2252d2dce" + }, + "BiocGenerics": { + "Package": "BiocGenerics", + "Version": "0.48.1", + "Source": "Bioconductor", + "Requirements": [ + "R", + "graphics", + "methods", + "stats", + "utils" + ], + "Hash": "e34278c65d7dffcc08f737bf0944ca9a" + }, + "BiocManager": { + "Package": "BiocManager", + "Version": "1.30.22", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "utils" + ], + "Hash": "d57e43105a1aa9cb54fdb4629725acb1" + }, + "BiocNeighbors": { + "Package": "BiocNeighbors", + "Version": "1.20.2", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "BiocParallel", + "Matrix", + "Rcpp", + "RcppHNSW", + "S4Vectors", + "methods", + "stats" + ], + "Hash": "c5c8ade5852fd3b25c66ec28873d00f1" + }, + "BiocParallel": { + "Package": "BiocParallel", + "Version": "1.36.0", + "Source": "Bioconductor", + "Requirements": [ + "BH", + "R", + "codetools", + "cpp11", + "futile.logger", + "methods", + "parallel", + "snow", + "stats", + "utils" + ], + "Hash": "6d1689ee8b65614ba6ef4012a67b663a" + }, + "BiocVersion": { + "Package": "BiocVersion", + "Version": "3.18.1", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "R" + ], + "Hash": "2ecaed86684f5fae76ed5530f9d29c4a" + }, + "DBI": { + "Package": "DBI", + "Version": "1.2.2", + "Source": "Repository" + }, + "DelayedArray": { + "Package": "DelayedArray", + "Version": "0.28.0", + "Source": "Bioconductor", + "Requirements": [ + "BiocGenerics", + "IRanges", + "Matrix", + "MatrixGenerics", + "R", + "S4Arrays", + "S4Vectors", + "SparseArray", + "methods", + "stats", + "stats4" + ], + "Hash": "0e5c84e543a3d04ce64c6f60ed46d7eb" + }, + "DelayedMatrixStats": { + "Package": "DelayedMatrixStats", + "Version": "1.24.0", + "Source": "Bioconductor", + "Requirements": [ + "DelayedArray", + "IRanges", + "Matrix", + "MatrixGenerics", + "S4Vectors", + "methods", + "sparseMatrixStats" + ], + "Hash": "71c2d178d33f9d91999f67dc2d53b747" + }, + "DropletUtils": { + "Package": "DropletUtils", + "Version": "1.22.0", + "Source": "Bioconductor", + "Requirements": [ + "BH", + "BiocGenerics", + "BiocParallel", + "DelayedArray", + "DelayedMatrixStats", + "GenomicRanges", + "HDF5Array", + "IRanges", + "Matrix", + "R.utils", + "Rcpp", + "Rhdf5lib", + "S4Vectors", + "SingleCellExperiment", + "SummarizedExperiment", + "beachmat", + "dqrng", + "edgeR", + "methods", + "rhdf5", + "scuttle", + "stats", + "utils" + ], + "Hash": "be3893d30c97591f1d3ec6f053830c3a" + }, + "GenomeInfoDb": { + "Package": "GenomeInfoDb", + "Version": "1.38.8", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "BiocGenerics", + "GenomeInfoDbData", + "IRanges", + "R", + "RCurl", + "S4Vectors", + "methods", + "stats", + "stats4", + "utils" + ], + "Hash": "155053909d2831bfac154a1118151d6b" + }, + "GenomeInfoDbData": { + "Package": "GenomeInfoDbData", + "Version": "1.2.11", + "Source": "Bioconductor", + "Requirements": [ + "R" + ], + "Hash": "10f32956181d1d46bd8402c93ac193e8" + }, + "GenomicRanges": { + "Package": "GenomicRanges", + "Version": "1.54.1", + "Source": "Bioconductor", + "Requirements": [ + "BiocGenerics", + "GenomeInfoDb", + "IRanges", + "R", + "S4Vectors", + "XVector", + "methods", + "stats", + "stats4", + "utils" + ], + "Hash": "7e0c1399af35369312d9c399454374e8" + }, + "HDF5Array": { + "Package": "HDF5Array", + "Version": "1.30.1", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "BiocGenerics", + "DelayedArray", + "IRanges", + "Matrix", + "R", + "Rhdf5lib", + "S4Arrays", + "S4Vectors", + "methods", + "rhdf5", + "rhdf5filters", + "stats", + "tools", + "utils" + ], + "Hash": "9b8deb4fd34fa439c16c829457d1968f" + }, + "IRanges": { + "Package": "IRanges", + "Version": "2.36.0", + "Source": "Bioconductor", + "Requirements": [ + "BiocGenerics", + "R", + "S4Vectors", + "methods", + "stats", + "stats4", + "utils" + ], + "Hash": "f98500eeb93e8a66ad65be955a848595" + }, + "MASS": { + "Package": "MASS", + "Version": "7.3-60.0.1", + "Source": "Repository" + }, + "Matrix": { + "Package": "Matrix", + "Version": "1.6-5", + "Source": "Repository" + }, + "MatrixGenerics": { + "Package": "MatrixGenerics", + "Version": "1.14.0", + "Source": "Bioconductor", + "Requirements": [ + "matrixStats", + "methods" + ], + "Hash": "088cd2077b5619fcb7b373b1a45174e7" + }, + "R.methodsS3": { + "Package": "R.methodsS3", + "Version": "1.8.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "utils" + ], + "Hash": "278c286fd6e9e75d0c2e8f731ea445c8" + }, + "R.oo": { + "Package": "R.oo", + "Version": "1.26.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "R.methodsS3", + "methods", + "utils" + ], + "Hash": "4fed809e53ddb5407b3da3d0f572e591" + }, + "R.utils": { + "Package": "R.utils", + "Version": "2.12.3", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "R.methodsS3", + "R.oo", + "methods", + "tools", + "utils" + ], + "Hash": "3dc2829b790254bfba21e60965787651" + }, + "R6": { + "Package": "R6", + "Version": "2.5.1", + "Source": "Repository" + }, + "RColorBrewer": { + "Package": "RColorBrewer", + "Version": "1.1-3", + "Source": "Repository" + }, + "RCurl": { + "Package": "RCurl", + "Version": "1.98-1.14", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "bitops", + "methods" + ], + "Hash": "47f648d288079d0c696804ad4e55197e" + }, + "Rcpp": { + "Package": "Rcpp", + "Version": "1.0.12", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "methods", + "utils" + ], + "Hash": "5ea2700d21e038ace58269ecdbeb9ec0" + }, + "RcppHNSW": { + "Package": "RcppHNSW", + "Version": "0.6.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "Rcpp", + "methods" + ], + "Hash": "1f2dc32c27746a35196aaf95adb357be" + }, + "Rhdf5lib": { + "Package": "Rhdf5lib", + "Version": "1.24.2", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "R" + ], + "Hash": "3cf103db29d75af0221d71946509a30c" + }, + "S4Arrays": { + "Package": "S4Arrays", + "Version": "1.2.1", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "BiocGenerics", + "IRanges", + "Matrix", + "R", + "S4Vectors", + "abind", + "crayon", + "methods", + "stats" + ], + "Hash": "3213a9826adb8f48e51af1e7b30fa568" + }, + "S4Vectors": { + "Package": "S4Vectors", + "Version": "0.40.2", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "BiocGenerics", + "R", + "methods", + "stats", + "stats4", + "utils" + ], + "Hash": "1716e201f81ced0f456dd5ec85fe20f8" + }, + "SingleCellExperiment": { + "Package": "SingleCellExperiment", + "Version": "1.24.0", + "Source": "Bioconductor", + "Requirements": [ + "BiocGenerics", + "DelayedArray", + "GenomicRanges", + "S4Vectors", + "SummarizedExperiment", + "methods", + "stats", + "utils" + ], + "Hash": "e21b3571ce76eb4dfe6bf7900960aa6a" + }, + "SparseArray": { + "Package": "SparseArray", + "Version": "1.2.4", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "BiocGenerics", + "IRanges", + "Matrix", + "MatrixGenerics", + "R", + "S4Arrays", + "S4Vectors", + "XVector", + "matrixStats", + "methods", + "stats" + ], + "Hash": "391092e7b81373ab624bd6471cebccd4" + }, + "SummarizedExperiment": { + "Package": "SummarizedExperiment", + "Version": "1.32.0", + "Source": "Bioconductor", + "Requirements": [ + "Biobase", + "BiocGenerics", + "DelayedArray", + "GenomeInfoDb", + "GenomicRanges", + "IRanges", + "Matrix", + "MatrixGenerics", + "R", + "S4Arrays", + "S4Vectors", + "methods", + "stats", + "tools", + "utils" + ], + "Hash": "caee529bf9710ff6fe1776612fcaa266" + }, + "XVector": { + "Package": "XVector", + "Version": "0.42.0", + "Source": "Bioconductor", + "Requirements": [ + "BiocGenerics", + "IRanges", + "R", + "S4Vectors", + "methods", + "tools", + "utils", + "zlibbioc" + ], + "Hash": "65c0b6bca03f88758f86ef0aa18c4873" + }, + "abind": { + "Package": "abind", + "Version": "1.4-5", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "methods", + "utils" + ], + "Hash": "4f57884290cc75ab22f4af9e9d4ca862" + }, + "askpass": { + "Package": "askpass", + "Version": "1.2.0", + "Source": "Repository" + }, + "backports": { + "Package": "backports", + "Version": "1.4.1", + "Source": "Repository" + }, + "base64enc": { + "Package": "base64enc", + "Version": "0.1-3", + "Source": "Repository" + }, + "beachmat": { + "Package": "beachmat", + "Version": "2.18.1", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "BiocGenerics", + "DelayedArray", + "Matrix", + "Rcpp", + "SparseArray", + "methods" + ], + "Hash": "c1c423ca7149d9e7f55d1e609342c2bd" + }, + "bit": { + "Package": "bit", + "Version": "4.0.5", + "Source": "Repository" + }, + "bit64": { + "Package": "bit64", + "Version": "4.0.5", + "Source": "Repository" + }, + "bitops": { + "Package": "bitops", + "Version": "1.0-7", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "b7d8d8ee39869c18d8846a184dd8a1af" + }, + "blob": { + "Package": "blob", + "Version": "1.2.4", + "Source": "Repository" + }, + "bluster": { + "Package": "bluster", + "Version": "1.12.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "BiocNeighbors", + "BiocParallel", + "Matrix", + "Rcpp", + "S4Vectors", + "cluster", + "igraph", + "methods", + "stats", + "utils" + ], + "Hash": "fca0d5ffad6380f13cad4d7855107aef" + }, + "broom": { + "Package": "broom", + "Version": "1.0.5", + "Source": "Repository" + }, + "bslib": { + "Package": "bslib", + "Version": "0.7.0", + "Source": "Repository" + }, + "cachem": { + "Package": "cachem", + "Version": "1.0.8", + "Source": "Repository" + }, + "callr": { + "Package": "callr", + "Version": "3.7.6", + "Source": "Repository" + }, + "cellranger": { + "Package": "cellranger", + "Version": "1.1.0", + "Source": "Repository" + }, + "cli": { + "Package": "cli", + "Version": "3.6.2", + "Source": "Repository" + }, + "clipr": { + "Package": "clipr", + "Version": "0.8.0", + "Source": "Repository" + }, + "cluster": { + "Package": "cluster", + "Version": "2.1.6", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "grDevices", + "graphics", + "stats", + "utils" + ], + "Hash": "0aaa05204035dc43ea0004b9c76611dd" + }, + "codetools": { + "Package": "codetools", + "Version": "0.2-20", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R" + ], + "Hash": "61e097f35917d342622f21cdc79c256e" + }, + "colorspace": { + "Package": "colorspace", + "Version": "2.1-0", + "Source": "Repository" + }, + "conflicted": { + "Package": "conflicted", + "Version": "1.2.0", + "Source": "Repository" + }, + "cpp11": { + "Package": "cpp11", + "Version": "0.4.7", + "Source": "Repository" + }, + "crayon": { + "Package": "crayon", + "Version": "1.5.2", + "Source": "Repository" + }, + "curl": { + "Package": "curl", + "Version": "5.2.1", + "Source": "Repository" + }, + "data.table": { + "Package": "data.table", + "Version": "1.15.4", + "Source": "Repository" + }, + "dbplyr": { + "Package": "dbplyr", + "Version": "2.5.0", + "Source": "Repository" + }, + "digest": { + "Package": "digest", + "Version": "0.6.35", + "Source": "Repository" + }, + "dplyr": { + "Package": "dplyr", + "Version": "1.1.4", + "Source": "Repository" + }, + "dqrng": { + "Package": "dqrng", + "Version": "0.3.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "BH", + "R", + "Rcpp", + "sitmo" + ], + "Hash": "824df2aeba88d701df5e79018b35b815" + }, + "dtplyr": { + "Package": "dtplyr", + "Version": "1.3.1", + "Source": "Repository" + }, + "edgeR": { + "Package": "edgeR", + "Version": "4.0.16", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "R", + "Rcpp", + "graphics", + "limma", + "locfit", + "methods", + "stats", + "utils" + ], + "Hash": "a0405c7890708dcb53809d46758800f4" + }, + "ellipsis": { + "Package": "ellipsis", + "Version": "0.3.2", + "Source": "Repository" + }, + "evaluate": { + "Package": "evaluate", + "Version": "0.23", + "Source": "Repository" + }, + "fansi": { + "Package": "fansi", + "Version": "1.0.6", + "Source": "Repository" + }, + "farver": { + "Package": "farver", + "Version": "2.1.1", + "Source": "Repository" + }, + "fastmap": { + "Package": "fastmap", + "Version": "1.1.1", + "Source": "Repository" + }, + "fishpond": { + "Package": "fishpond", + "Version": "2.8.0", + "Source": "Bioconductor", + "Requirements": [ + "GenomicRanges", + "IRanges", + "Matrix", + "S4Vectors", + "SingleCellExperiment", + "SummarizedExperiment", + "abind", + "graphics", + "gtools", + "jsonlite", + "matrixStats", + "methods", + "qvalue", + "stats", + "svMisc", + "utils" + ], + "Hash": "60ebe3366ccb6c1a11a99682f56f2a2f" + }, + "flexmix": { + "Package": "flexmix", + "Version": "2.3-19", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "grDevices", + "graphics", + "grid", + "lattice", + "methods", + "modeltools", + "nnet", + "stats", + "stats4", + "utils" + ], + "Hash": "0cb3c4b251c2d3fd5923d3e7e6021ee2" + }, + "fontawesome": { + "Package": "fontawesome", + "Version": "0.5.2", + "Source": "Repository" + }, + "forcats": { + "Package": "forcats", + "Version": "1.0.0", + "Source": "Repository" + }, + "formatR": { + "Package": "formatR", + "Version": "1.14", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R" + ], + "Hash": "63cb26d12517c7863f5abb006c5e0f25" + }, + "fs": { + "Package": "fs", + "Version": "1.6.3", + "Source": "Repository" + }, + "futile.logger": { + "Package": "futile.logger", + "Version": "1.4.3", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "futile.options", + "lambda.r", + "utils" + ], + "Hash": "99f0ace8c05ec7d3683d27083c4f1e7e" + }, + "futile.options": { + "Package": "futile.options", + "Version": "1.0.1", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R" + ], + "Hash": "0d9bf02413ddc2bbe8da9ce369dcdd2b" + }, + "gargle": { + "Package": "gargle", + "Version": "1.5.2", + "Source": "Repository" + }, + "generics": { + "Package": "generics", + "Version": "0.1.3", + "Source": "Repository" + }, + "getopt": { + "Package": "getopt", + "Version": "1.20.4", + "Source": "Repository" + }, + "ggplot2": { + "Package": "ggplot2", + "Version": "3.5.0", + "Source": "Repository" + }, + "glue": { + "Package": "glue", + "Version": "1.7.0", + "Source": "Repository" + }, + "googledrive": { + "Package": "googledrive", + "Version": "2.1.1", + "Source": "Repository" + }, + "googlesheets4": { + "Package": "googlesheets4", + "Version": "1.1.1", + "Source": "Repository" + }, + "grDevices": { + "Package": "grDevices", + "Version": "4.3.3", + "Source": "R" + }, + "graphics": { + "Package": "graphics", + "Version": "4.3.3", + "Source": "R" + }, + "grid": { + "Package": "grid", + "Version": "4.3.3", + "Source": "R" + }, + "gtable": { + "Package": "gtable", + "Version": "0.3.5", + "Source": "Repository" + }, + "gtools": { + "Package": "gtools", + "Version": "3.9.5", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "methods", + "stats", + "utils" + ], + "Hash": "588d091c35389f1f4a9d533c8d709b35" + }, + "haven": { + "Package": "haven", + "Version": "2.5.4", + "Source": "Repository" + }, + "highr": { + "Package": "highr", + "Version": "0.10", + "Source": "Repository" + }, + "hms": { + "Package": "hms", + "Version": "1.1.3", + "Source": "Repository" + }, + "htmltools": { + "Package": "htmltools", + "Version": "0.5.8.1", + "Source": "Repository" + }, + "httr": { + "Package": "httr", + "Version": "1.4.7", + "Source": "Repository" + }, + "ids": { + "Package": "ids", + "Version": "1.0.1", + "Source": "Repository" + }, + "igraph": { + "Package": "igraph", + "Version": "2.0.3", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "Matrix", + "R", + "cli", + "cpp11", + "grDevices", + "graphics", + "lifecycle", + "magrittr", + "methods", + "pkgconfig", + "rlang", + "stats", + "utils", + "vctrs" + ], + "Hash": "c3b7d801d722e26e4cd888e042bf9af5" + }, + "isoband": { + "Package": "isoband", + "Version": "0.2.7", + "Source": "Repository" + }, + "jquerylib": { + "Package": "jquerylib", + "Version": "0.1.4", + "Source": "Repository" + }, + "jsonlite": { + "Package": "jsonlite", + "Version": "1.8.8", + "Source": "Repository" + }, + "knitr": { + "Package": "knitr", + "Version": "1.46", + "Source": "Repository" + }, + "labeling": { + "Package": "labeling", + "Version": "0.4.3", + "Source": "Repository" + }, + "lambda.r": { + "Package": "lambda.r", + "Version": "1.2.4", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "formatR" + ], + "Hash": "b1e925c4b9ffeb901bacf812cbe9a6ad" + }, + "lattice": { + "Package": "lattice", + "Version": "0.22-6", + "Source": "Repository" + }, + "lifecycle": { + "Package": "lifecycle", + "Version": "1.0.4", + "Source": "Repository" + }, + "limma": { + "Package": "limma", + "Version": "3.58.1", + "Source": "Bioconductor", + "Requirements": [ + "R", + "grDevices", + "graphics", + "methods", + "statmod", + "stats", + "utils" + ], + "Hash": "74c3b64358e0be7edc3ecd130816dd3f" + }, + "locfit": { + "Package": "locfit", + "Version": "1.5-9.9", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "lattice" + ], + "Hash": "3885127e04b35dafded049075057ad83" + }, + "lubridate": { + "Package": "lubridate", + "Version": "1.9.3", + "Source": "Repository" + }, + "magrittr": { + "Package": "magrittr", + "Version": "2.0.3", + "Source": "Repository" + }, + "matrixStats": { + "Package": "matrixStats", + "Version": "1.3.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R" + ], + "Hash": "4b3ea27a19d669c0405b38134d89a9d1" + }, + "memoise": { + "Package": "memoise", + "Version": "2.0.1", + "Source": "Repository" + }, + "methods": { + "Package": "methods", + "Version": "4.3.3", + "Source": "R" + }, + "mgcv": { + "Package": "mgcv", + "Version": "1.9-1", + "Source": "Repository" + }, + "miQC": { + "Package": "miQC", + "Version": "1.10.0", + "Source": "Bioconductor", + "Requirements": [ + "R", + "SingleCellExperiment", + "flexmix", + "ggplot2", + "splines" + ], + "Hash": "5d3660451d88509307ce0b0e48748109" + }, + "mime": { + "Package": "mime", + "Version": "0.12", + "Source": "Repository" + }, + "modelr": { + "Package": "modelr", + "Version": "0.1.11", + "Source": "Repository" + }, + "modeltools": { + "Package": "modeltools", + "Version": "0.2-23", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "methods", + "stats", + "stats4" + ], + "Hash": "f5a957c02222589bdf625a67be68b2a9" + }, + "munsell": { + "Package": "munsell", + "Version": "0.5.1", + "Source": "Repository" + }, + "nlme": { + "Package": "nlme", + "Version": "3.1-164", + "Source": "Repository" + }, + "nnet": { + "Package": "nnet", + "Version": "7.3-19", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "stats", + "utils" + ], + "Hash": "2c797b46eea7fb58ede195bc0b1f1138" + }, + "openssl": { + "Package": "openssl", + "Version": "2.1.2", + "Source": "Repository" + }, + "optparse": { + "Package": "optparse", + "Version": "1.7.5", + "Source": "Repository" + }, + "pillar": { + "Package": "pillar", + "Version": "1.9.0", + "Source": "Repository" + }, + "pkgconfig": { + "Package": "pkgconfig", + "Version": "2.0.3", + "Source": "Repository" + }, + "plyr": { + "Package": "plyr", + "Version": "1.8.9", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "Rcpp" + ], + "Hash": "6b8177fd19982f0020743fadbfdbd933" + }, + "prettyunits": { + "Package": "prettyunits", + "Version": "1.2.0", + "Source": "Repository" + }, + "processx": { + "Package": "processx", + "Version": "3.8.4", + "Source": "Repository" + }, + "progress": { + "Package": "progress", + "Version": "1.2.3", + "Source": "Repository" + }, + "ps": { + "Package": "ps", + "Version": "1.7.6", + "Source": "Repository" + }, + "purrr": { + "Package": "purrr", + "Version": "1.0.2", + "Source": "Repository" + }, + "qvalue": { + "Package": "qvalue", + "Version": "2.34.0", + "Source": "Bioconductor", + "Requirements": [ + "R", + "ggplot2", + "grid", + "reshape2", + "splines" + ], + "Hash": "76fc42834c44b69e4021f6ade524d299" + }, + "ragg": { + "Package": "ragg", + "Version": "1.3.0", + "Source": "Repository" + }, + "rappdirs": { + "Package": "rappdirs", + "Version": "0.3.3", + "Source": "Repository" + }, + "readr": { + "Package": "readr", + "Version": "2.1.5", + "Source": "Repository" + }, + "readxl": { + "Package": "readxl", + "Version": "1.4.3", + "Source": "Repository" + }, + "rematch": { + "Package": "rematch", + "Version": "2.0.0", + "Source": "Repository" + }, + "rematch2": { + "Package": "rematch2", + "Version": "2.1.2", + "Source": "Repository" + }, + "renv": { + "Package": "renv", + "Version": "1.0.7", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "utils" + ], + "Hash": "397b7b2a265bc5a7a06852524dabae20" + }, + "reprex": { + "Package": "reprex", + "Version": "2.1.0", + "Source": "Repository" + }, + "reshape2": { + "Package": "reshape2", + "Version": "1.4.4", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "Rcpp", + "plyr", + "stringr" + ], + "Hash": "bb5996d0bd962d214a11140d77589917" + }, + "rhdf5": { + "Package": "rhdf5", + "Version": "2.46.1", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "R", + "Rhdf5lib", + "S4Vectors", + "methods", + "rhdf5filters" + ], + "Hash": "b0a244022c3427cd8213c33804c6b5de" + }, + "rhdf5filters": { + "Package": "rhdf5filters", + "Version": "1.14.1", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "Rhdf5lib" + ], + "Hash": "d27a2f6a89def6388fad5b0aae026220" + }, + "rlang": { + "Package": "rlang", + "Version": "1.1.3", + "Source": "Repository" + }, + "rmarkdown": { + "Package": "rmarkdown", + "Version": "2.26", + "Source": "Repository" + }, + "rstudioapi": { + "Package": "rstudioapi", + "Version": "0.16.0", + "Source": "Repository" + }, + "rvest": { + "Package": "rvest", + "Version": "1.0.4", + "Source": "Repository" + }, + "sass": { + "Package": "sass", + "Version": "0.4.9", + "Source": "Repository" + }, + "scales": { + "Package": "scales", + "Version": "1.3.0", + "Source": "Repository" + }, + "scuttle": { + "Package": "scuttle", + "Version": "1.12.0", + "Source": "Bioconductor", + "Requirements": [ + "BiocGenerics", + "BiocParallel", + "DelayedArray", + "DelayedMatrixStats", + "GenomicRanges", + "Matrix", + "Rcpp", + "S4Vectors", + "SingleCellExperiment", + "SummarizedExperiment", + "beachmat", + "methods", + "stats", + "utils" + ], + "Hash": "1412c4b6dfd8de528e1101e493e66a02" + }, + "selectr": { + "Package": "selectr", + "Version": "0.4-2", + "Source": "Repository" + }, + "sitmo": { + "Package": "sitmo", + "Version": "2.0.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "Rcpp" + ], + "Hash": "c956d93f6768a9789edbc13072b70c78" + }, + "snow": { + "Package": "snow", + "Version": "0.4-4", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "utils" + ], + "Hash": "40b74690debd20c57d93d8c246b305d4" + }, + "sparseMatrixStats": { + "Package": "sparseMatrixStats", + "Version": "1.14.0", + "Source": "Bioconductor", + "Requirements": [ + "Matrix", + "MatrixGenerics", + "Rcpp", + "matrixStats", + "methods" + ], + "Hash": "49383d0f6c6152ff7cb594f254c23cc8" + }, + "splines": { + "Package": "splines", + "Version": "4.3.3", + "Source": "R" + }, + "statmod": { + "Package": "statmod", + "Version": "1.5.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "graphics", + "stats" + ], + "Hash": "26e158d12052c279bdd4ba858b80fb1f" + }, + "stats": { + "Package": "stats", + "Version": "4.3.3", + "Source": "R" + }, + "stringi": { + "Package": "stringi", + "Version": "1.8.3", + "Source": "Repository" + }, + "stringr": { + "Package": "stringr", + "Version": "1.5.1", + "Source": "Repository" + }, + "svMisc": { + "Package": "svMisc", + "Version": "1.2.3", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "methods", + "stats", + "tools", + "utils" + ], + "Hash": "b13f5680860f67c32ccb006ad38f24f4" + }, + "sys": { + "Package": "sys", + "Version": "3.4.2", + "Source": "Repository" + }, + "systemfonts": { + "Package": "systemfonts", + "Version": "1.0.6", + "Source": "Repository" + }, + "textshaping": { + "Package": "textshaping", + "Version": "0.3.7", + "Source": "Repository" + }, + "tibble": { + "Package": "tibble", + "Version": "3.2.1", + "Source": "Repository" + }, + "tidyr": { + "Package": "tidyr", + "Version": "1.3.1", + "Source": "Repository" + }, + "tidyselect": { + "Package": "tidyselect", + "Version": "1.2.1", + "Source": "Repository" + }, + "tidyverse": { + "Package": "tidyverse", + "Version": "2.0.0", + "Source": "Repository" + }, + "timechange": { + "Package": "timechange", + "Version": "0.3.0", + "Source": "Repository" + }, + "tinytex": { + "Package": "tinytex", + "Version": "0.50", + "Source": "Repository" + }, + "tools": { + "Package": "tools", + "Version": "4.3.3", + "Source": "R" + }, + "tximport": { + "Package": "tximport", + "Version": "1.30.0", + "Source": "Bioconductor", + "Requirements": [ + "methods", + "stats", + "utils" + ], + "Hash": "6e9621b0f1bf9398255f32c7000a7e16" + }, + "tzdb": { + "Package": "tzdb", + "Version": "0.4.0", + "Source": "Repository" + }, + "utf8": { + "Package": "utf8", + "Version": "1.2.4", + "Source": "Repository" + }, + "utils": { + "Package": "utils", + "Version": "4.3.3", + "Source": "R" + }, + "uuid": { + "Package": "uuid", + "Version": "1.2-0", + "Source": "Repository" + }, + "vctrs": { + "Package": "vctrs", + "Version": "0.6.5", + "Source": "Repository" + }, + "viridisLite": { + "Package": "viridisLite", + "Version": "0.4.2", + "Source": "Repository" + }, + "vroom": { + "Package": "vroom", + "Version": "1.6.5", + "Source": "Repository" + }, + "withr": { + "Package": "withr", + "Version": "3.0.0", + "Source": "Repository" + }, + "xfun": { + "Package": "xfun", + "Version": "0.43", + "Source": "Repository" + }, + "xml2": { + "Package": "xml2", + "Version": "1.3.6", + "Source": "Repository" + }, + "yaml": { + "Package": "yaml", + "Version": "2.3.8", + "Source": "Repository" + }, + "zlibbioc": { + "Package": "zlibbioc", + "Version": "1.48.2", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Hash": "2344be62c2da4d9e9942b5d8db346e59" + } + } +} diff --git a/docker/renv_zellkonverter.lock b/docker/renv_zellkonverter.lock new file mode 100644 index 00000000..9fb8bde3 --- /dev/null +++ b/docker/renv_zellkonverter.lock @@ -0,0 +1,1410 @@ +{ + "R": { + "Version": "4.3.3", + "Repositories": [ + { + "Name": "BioCsoft", + "URL": "https://bioconductor.org/packages/3.18/bioc" + }, + { + "Name": "BioCann", + "URL": "https://bioconductor.org/packages/3.18/data/annotation" + }, + { + "Name": "BioCexp", + "URL": "https://bioconductor.org/packages/3.18/data/experiment" + }, + { + "Name": "BioCworkflows", + "URL": "https://bioconductor.org/packages/3.18/workflows" + }, + { + "Name": "BioCbooks", + "URL": "https://bioconductor.org/packages/3.18/books" + }, + { + "Name": "CRAN", + "URL": "https://p3m.dev/cran/latest" + } + ] + }, + "Bioconductor": { + "Version": "3.18" + }, + "Packages": { + "BH": { + "Package": "BH", + "Version": "1.84.0-0", + "Source": "Repository", + "Repository": "RSPM", + "Hash": "a8235afbcd6316e6e91433ea47661013" + }, + "Biobase": { + "Package": "Biobase", + "Version": "2.62.0", + "Source": "Repository" + }, + "BiocGenerics": { + "Package": "BiocGenerics", + "Version": "0.48.1", + "Source": "Repository" + }, + "BiocManager": { + "Package": "BiocManager", + "Version": "1.30.22", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "utils" + ], + "Hash": "d57e43105a1aa9cb54fdb4629725acb1" + }, + "BiocNeighbors": { + "Package": "BiocNeighbors", + "Version": "1.20.2", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "BiocParallel", + "Matrix", + "Rcpp", + "RcppHNSW", + "S4Vectors", + "methods", + "stats" + ], + "Hash": "c5c8ade5852fd3b25c66ec28873d00f1" + }, + "BiocParallel": { + "Package": "BiocParallel", + "Version": "1.36.0", + "Source": "Bioconductor", + "Requirements": [ + "BH", + "R", + "codetools", + "cpp11", + "futile.logger", + "methods", + "parallel", + "snow", + "stats", + "utils" + ], + "Hash": "6d1689ee8b65614ba6ef4012a67b663a" + }, + "BiocVersion": { + "Package": "BiocVersion", + "Version": "3.18.1", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "R" + ], + "Hash": "2ecaed86684f5fae76ed5530f9d29c4a" + }, + "DBI": { + "Package": "DBI", + "Version": "1.2.2", + "Source": "Repository" + }, + "DelayedArray": { + "Package": "DelayedArray", + "Version": "0.28.0", + "Source": "Repository" + }, + "DelayedMatrixStats": { + "Package": "DelayedMatrixStats", + "Version": "1.24.0", + "Source": "Bioconductor", + "Requirements": [ + "DelayedArray", + "IRanges", + "Matrix", + "MatrixGenerics", + "S4Vectors", + "methods", + "sparseMatrixStats" + ], + "Hash": "71c2d178d33f9d91999f67dc2d53b747" + }, + "DropletUtils": { + "Package": "DropletUtils", + "Version": "1.22.0", + "Source": "Bioconductor", + "Requirements": [ + "BH", + "BiocGenerics", + "BiocParallel", + "DelayedArray", + "DelayedMatrixStats", + "GenomicRanges", + "HDF5Array", + "IRanges", + "Matrix", + "R.utils", + "Rcpp", + "Rhdf5lib", + "S4Vectors", + "SingleCellExperiment", + "SummarizedExperiment", + "beachmat", + "dqrng", + "edgeR", + "methods", + "rhdf5", + "scuttle", + "stats", + "utils" + ], + "Hash": "be3893d30c97591f1d3ec6f053830c3a" + }, + "GenomeInfoDb": { + "Package": "GenomeInfoDb", + "Version": "1.38.8", + "Source": "Repository" + }, + "GenomeInfoDbData": { + "Package": "GenomeInfoDbData", + "Version": "1.2.11", + "Source": "Repository" + }, + "GenomicRanges": { + "Package": "GenomicRanges", + "Version": "1.54.1", + "Source": "Repository" + }, + "HDF5Array": { + "Package": "HDF5Array", + "Version": "1.30.1", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "BiocGenerics", + "DelayedArray", + "IRanges", + "Matrix", + "R", + "Rhdf5lib", + "S4Arrays", + "S4Vectors", + "methods", + "rhdf5", + "rhdf5filters", + "stats", + "tools", + "utils" + ], + "Hash": "9b8deb4fd34fa439c16c829457d1968f" + }, + "IRanges": { + "Package": "IRanges", + "Version": "2.36.0", + "Source": "Repository" + }, + "MASS": { + "Package": "MASS", + "Version": "7.3-60.0.1", + "Source": "Repository" + }, + "Matrix": { + "Package": "Matrix", + "Version": "1.6-5", + "Source": "Repository" + }, + "MatrixGenerics": { + "Package": "MatrixGenerics", + "Version": "1.14.0", + "Source": "Repository" + }, + "R.methodsS3": { + "Package": "R.methodsS3", + "Version": "1.8.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "utils" + ], + "Hash": "278c286fd6e9e75d0c2e8f731ea445c8" + }, + "R.oo": { + "Package": "R.oo", + "Version": "1.26.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "R.methodsS3", + "methods", + "utils" + ], + "Hash": "4fed809e53ddb5407b3da3d0f572e591" + }, + "R.utils": { + "Package": "R.utils", + "Version": "2.12.3", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "R.methodsS3", + "R.oo", + "methods", + "tools", + "utils" + ], + "Hash": "3dc2829b790254bfba21e60965787651" + }, + "R6": { + "Package": "R6", + "Version": "2.5.1", + "Source": "Repository" + }, + "RColorBrewer": { + "Package": "RColorBrewer", + "Version": "1.1-3", + "Source": "Repository" + }, + "RCurl": { + "Package": "RCurl", + "Version": "1.98-1.14", + "Source": "Repository" + }, + "Rcpp": { + "Package": "Rcpp", + "Version": "1.0.12", + "Source": "Repository" + }, + "RcppHNSW": { + "Package": "RcppHNSW", + "Version": "0.6.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "Rcpp", + "methods" + ], + "Hash": "1f2dc32c27746a35196aaf95adb357be" + }, + "RcppTOML": { + "Package": "RcppTOML", + "Version": "0.2.2", + "Source": "Repository" + }, + "Rhdf5lib": { + "Package": "Rhdf5lib", + "Version": "1.24.2", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "R" + ], + "Hash": "3cf103db29d75af0221d71946509a30c" + }, + "S4Arrays": { + "Package": "S4Arrays", + "Version": "1.2.1", + "Source": "Repository" + }, + "S4Vectors": { + "Package": "S4Vectors", + "Version": "0.40.2", + "Source": "Repository" + }, + "SingleCellExperiment": { + "Package": "SingleCellExperiment", + "Version": "1.24.0", + "Source": "Repository" + }, + "SparseArray": { + "Package": "SparseArray", + "Version": "1.2.4", + "Source": "Repository" + }, + "SummarizedExperiment": { + "Package": "SummarizedExperiment", + "Version": "1.32.0", + "Source": "Repository" + }, + "XVector": { + "Package": "XVector", + "Version": "0.42.0", + "Source": "Repository" + }, + "abind": { + "Package": "abind", + "Version": "1.4-5", + "Source": "Repository" + }, + "askpass": { + "Package": "askpass", + "Version": "1.2.0", + "Source": "Repository" + }, + "backports": { + "Package": "backports", + "Version": "1.4.1", + "Source": "Repository" + }, + "base64enc": { + "Package": "base64enc", + "Version": "0.1-3", + "Source": "Repository" + }, + "basilisk": { + "Package": "basilisk", + "Version": "1.14.3", + "Source": "Repository" + }, + "basilisk.utils": { + "Package": "basilisk.utils", + "Version": "1.14.1", + "Source": "Repository" + }, + "beachmat": { + "Package": "beachmat", + "Version": "2.18.1", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "BiocGenerics", + "DelayedArray", + "Matrix", + "Rcpp", + "SparseArray", + "methods" + ], + "Hash": "c1c423ca7149d9e7f55d1e609342c2bd" + }, + "bit": { + "Package": "bit", + "Version": "4.0.5", + "Source": "Repository" + }, + "bit64": { + "Package": "bit64", + "Version": "4.0.5", + "Source": "Repository" + }, + "bitops": { + "Package": "bitops", + "Version": "1.0-7", + "Source": "Repository" + }, + "blob": { + "Package": "blob", + "Version": "1.2.4", + "Source": "Repository" + }, + "bluster": { + "Package": "bluster", + "Version": "1.12.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "BiocNeighbors", + "BiocParallel", + "Matrix", + "Rcpp", + "S4Vectors", + "cluster", + "igraph", + "methods", + "stats", + "utils" + ], + "Hash": "fca0d5ffad6380f13cad4d7855107aef" + }, + "broom": { + "Package": "broom", + "Version": "1.0.5", + "Source": "Repository" + }, + "bslib": { + "Package": "bslib", + "Version": "0.7.0", + "Source": "Repository" + }, + "cachem": { + "Package": "cachem", + "Version": "1.0.8", + "Source": "Repository" + }, + "callr": { + "Package": "callr", + "Version": "3.7.6", + "Source": "Repository" + }, + "cellranger": { + "Package": "cellranger", + "Version": "1.1.0", + "Source": "Repository" + }, + "cli": { + "Package": "cli", + "Version": "3.6.2", + "Source": "Repository" + }, + "clipr": { + "Package": "clipr", + "Version": "0.8.0", + "Source": "Repository" + }, + "cluster": { + "Package": "cluster", + "Version": "2.1.6", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "grDevices", + "graphics", + "stats", + "utils" + ], + "Hash": "0aaa05204035dc43ea0004b9c76611dd" + }, + "codetools": { + "Package": "codetools", + "Version": "0.2-20", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R" + ], + "Hash": "61e097f35917d342622f21cdc79c256e" + }, + "colorspace": { + "Package": "colorspace", + "Version": "2.1-0", + "Source": "Repository" + }, + "conflicted": { + "Package": "conflicted", + "Version": "1.2.0", + "Source": "Repository" + }, + "cpp11": { + "Package": "cpp11", + "Version": "0.4.7", + "Source": "Repository" + }, + "crayon": { + "Package": "crayon", + "Version": "1.5.2", + "Source": "Repository" + }, + "curl": { + "Package": "curl", + "Version": "5.2.1", + "Source": "Repository" + }, + "data.table": { + "Package": "data.table", + "Version": "1.15.4", + "Source": "Repository" + }, + "dbplyr": { + "Package": "dbplyr", + "Version": "2.5.0", + "Source": "Repository" + }, + "digest": { + "Package": "digest", + "Version": "0.6.35", + "Source": "Repository" + }, + "dir.expiry": { + "Package": "dir.expiry", + "Version": "1.10.0", + "Source": "Repository" + }, + "dplyr": { + "Package": "dplyr", + "Version": "1.1.4", + "Source": "Repository" + }, + "dqrng": { + "Package": "dqrng", + "Version": "0.3.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "BH", + "R", + "Rcpp", + "sitmo" + ], + "Hash": "824df2aeba88d701df5e79018b35b815" + }, + "dtplyr": { + "Package": "dtplyr", + "Version": "1.3.1", + "Source": "Repository" + }, + "edgeR": { + "Package": "edgeR", + "Version": "4.0.16", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "R", + "Rcpp", + "graphics", + "limma", + "locfit", + "methods", + "stats", + "utils" + ], + "Hash": "a0405c7890708dcb53809d46758800f4" + }, + "ellipsis": { + "Package": "ellipsis", + "Version": "0.3.2", + "Source": "Repository" + }, + "evaluate": { + "Package": "evaluate", + "Version": "0.23", + "Source": "Repository" + }, + "fansi": { + "Package": "fansi", + "Version": "1.0.6", + "Source": "Repository" + }, + "farver": { + "Package": "farver", + "Version": "2.1.1", + "Source": "Repository" + }, + "fastmap": { + "Package": "fastmap", + "Version": "1.1.1", + "Source": "Repository" + }, + "filelock": { + "Package": "filelock", + "Version": "1.0.3", + "Source": "Repository" + }, + "fishpond": { + "Package": "fishpond", + "Version": "2.8.0", + "Source": "Bioconductor", + "Requirements": [ + "GenomicRanges", + "IRanges", + "Matrix", + "S4Vectors", + "SingleCellExperiment", + "SummarizedExperiment", + "abind", + "graphics", + "gtools", + "jsonlite", + "matrixStats", + "methods", + "qvalue", + "stats", + "svMisc", + "utils" + ], + "Hash": "60ebe3366ccb6c1a11a99682f56f2a2f" + }, + "flexmix": { + "Package": "flexmix", + "Version": "2.3-19", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "grDevices", + "graphics", + "grid", + "lattice", + "methods", + "modeltools", + "nnet", + "stats", + "stats4", + "utils" + ], + "Hash": "0cb3c4b251c2d3fd5923d3e7e6021ee2" + }, + "fontawesome": { + "Package": "fontawesome", + "Version": "0.5.2", + "Source": "Repository" + }, + "forcats": { + "Package": "forcats", + "Version": "1.0.0", + "Source": "Repository" + }, + "formatR": { + "Package": "formatR", + "Version": "1.14", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R" + ], + "Hash": "63cb26d12517c7863f5abb006c5e0f25" + }, + "fs": { + "Package": "fs", + "Version": "1.6.3", + "Source": "Repository" + }, + "futile.logger": { + "Package": "futile.logger", + "Version": "1.4.3", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "futile.options", + "lambda.r", + "utils" + ], + "Hash": "99f0ace8c05ec7d3683d27083c4f1e7e" + }, + "futile.options": { + "Package": "futile.options", + "Version": "1.0.1", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R" + ], + "Hash": "0d9bf02413ddc2bbe8da9ce369dcdd2b" + }, + "gargle": { + "Package": "gargle", + "Version": "1.5.2", + "Source": "Repository" + }, + "generics": { + "Package": "generics", + "Version": "0.1.3", + "Source": "Repository" + }, + "getopt": { + "Package": "getopt", + "Version": "1.20.4", + "Source": "Repository" + }, + "ggplot2": { + "Package": "ggplot2", + "Version": "3.5.0", + "Source": "Repository" + }, + "glue": { + "Package": "glue", + "Version": "1.7.0", + "Source": "Repository" + }, + "googledrive": { + "Package": "googledrive", + "Version": "2.1.1", + "Source": "Repository" + }, + "googlesheets4": { + "Package": "googlesheets4", + "Version": "1.1.1", + "Source": "Repository" + }, + "grDevices": { + "Package": "grDevices", + "Version": "4.3.3", + "Source": "R" + }, + "graphics": { + "Package": "graphics", + "Version": "4.3.3", + "Source": "R" + }, + "grid": { + "Package": "grid", + "Version": "4.3.3", + "Source": "R" + }, + "gtable": { + "Package": "gtable", + "Version": "0.3.5", + "Source": "Repository" + }, + "gtools": { + "Package": "gtools", + "Version": "3.9.5", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "methods", + "stats", + "utils" + ], + "Hash": "588d091c35389f1f4a9d533c8d709b35" + }, + "haven": { + "Package": "haven", + "Version": "2.5.4", + "Source": "Repository" + }, + "here": { + "Package": "here", + "Version": "1.0.1", + "Source": "Repository" + }, + "highr": { + "Package": "highr", + "Version": "0.10", + "Source": "Repository" + }, + "hms": { + "Package": "hms", + "Version": "1.1.3", + "Source": "Repository" + }, + "htmltools": { + "Package": "htmltools", + "Version": "0.5.8.1", + "Source": "Repository" + }, + "httr": { + "Package": "httr", + "Version": "1.4.7", + "Source": "Repository" + }, + "ids": { + "Package": "ids", + "Version": "1.0.1", + "Source": "Repository" + }, + "igraph": { + "Package": "igraph", + "Version": "2.0.3", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "Matrix", + "R", + "cli", + "cpp11", + "grDevices", + "graphics", + "lifecycle", + "magrittr", + "methods", + "pkgconfig", + "rlang", + "stats", + "utils", + "vctrs" + ], + "Hash": "c3b7d801d722e26e4cd888e042bf9af5" + }, + "isoband": { + "Package": "isoband", + "Version": "0.2.7", + "Source": "Repository" + }, + "jquerylib": { + "Package": "jquerylib", + "Version": "0.1.4", + "Source": "Repository" + }, + "jsonlite": { + "Package": "jsonlite", + "Version": "1.8.8", + "Source": "Repository" + }, + "knitr": { + "Package": "knitr", + "Version": "1.46", + "Source": "Repository" + }, + "labeling": { + "Package": "labeling", + "Version": "0.4.3", + "Source": "Repository" + }, + "lambda.r": { + "Package": "lambda.r", + "Version": "1.2.4", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "formatR" + ], + "Hash": "b1e925c4b9ffeb901bacf812cbe9a6ad" + }, + "lattice": { + "Package": "lattice", + "Version": "0.22-6", + "Source": "Repository" + }, + "lifecycle": { + "Package": "lifecycle", + "Version": "1.0.4", + "Source": "Repository" + }, + "limma": { + "Package": "limma", + "Version": "3.58.1", + "Source": "Bioconductor", + "Requirements": [ + "R", + "grDevices", + "graphics", + "methods", + "statmod", + "stats", + "utils" + ], + "Hash": "74c3b64358e0be7edc3ecd130816dd3f" + }, + "locfit": { + "Package": "locfit", + "Version": "1.5-9.9", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "lattice" + ], + "Hash": "3885127e04b35dafded049075057ad83" + }, + "lubridate": { + "Package": "lubridate", + "Version": "1.9.3", + "Source": "Repository" + }, + "magrittr": { + "Package": "magrittr", + "Version": "2.0.3", + "Source": "Repository" + }, + "matrixStats": { + "Package": "matrixStats", + "Version": "1.3.0", + "Source": "Repository" + }, + "memoise": { + "Package": "memoise", + "Version": "2.0.1", + "Source": "Repository" + }, + "methods": { + "Package": "methods", + "Version": "4.3.3", + "Source": "R" + }, + "mgcv": { + "Package": "mgcv", + "Version": "1.9-1", + "Source": "Repository" + }, + "miQC": { + "Package": "miQC", + "Version": "1.10.0", + "Source": "Bioconductor", + "Requirements": [ + "R", + "SingleCellExperiment", + "flexmix", + "ggplot2", + "splines" + ], + "Hash": "5d3660451d88509307ce0b0e48748109" + }, + "mime": { + "Package": "mime", + "Version": "0.12", + "Source": "Repository" + }, + "modelr": { + "Package": "modelr", + "Version": "0.1.11", + "Source": "Repository" + }, + "modeltools": { + "Package": "modeltools", + "Version": "0.2-23", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "methods", + "stats", + "stats4" + ], + "Hash": "f5a957c02222589bdf625a67be68b2a9" + }, + "munsell": { + "Package": "munsell", + "Version": "0.5.1", + "Source": "Repository" + }, + "nlme": { + "Package": "nlme", + "Version": "3.1-164", + "Source": "Repository" + }, + "nnet": { + "Package": "nnet", + "Version": "7.3-19", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "stats", + "utils" + ], + "Hash": "2c797b46eea7fb58ede195bc0b1f1138" + }, + "openssl": { + "Package": "openssl", + "Version": "2.1.2", + "Source": "Repository" + }, + "optparse": { + "Package": "optparse", + "Version": "1.7.5", + "Source": "Repository" + }, + "parallel": { + "Package": "parallel", + "Version": "4.3.3", + "Source": "R" + }, + "pillar": { + "Package": "pillar", + "Version": "1.9.0", + "Source": "Repository" + }, + "pkgconfig": { + "Package": "pkgconfig", + "Version": "2.0.3", + "Source": "Repository" + }, + "plyr": { + "Package": "plyr", + "Version": "1.8.9", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "Rcpp" + ], + "Hash": "6b8177fd19982f0020743fadbfdbd933" + }, + "png": { + "Package": "png", + "Version": "0.1-8", + "Source": "Repository" + }, + "prettyunits": { + "Package": "prettyunits", + "Version": "1.2.0", + "Source": "Repository" + }, + "processx": { + "Package": "processx", + "Version": "3.8.4", + "Source": "Repository" + }, + "progress": { + "Package": "progress", + "Version": "1.2.3", + "Source": "Repository" + }, + "ps": { + "Package": "ps", + "Version": "1.7.6", + "Source": "Repository" + }, + "purrr": { + "Package": "purrr", + "Version": "1.0.2", + "Source": "Repository" + }, + "qvalue": { + "Package": "qvalue", + "Version": "2.34.0", + "Source": "Bioconductor", + "Requirements": [ + "R", + "ggplot2", + "grid", + "reshape2", + "splines" + ], + "Hash": "76fc42834c44b69e4021f6ade524d299" + }, + "ragg": { + "Package": "ragg", + "Version": "1.3.0", + "Source": "Repository" + }, + "rappdirs": { + "Package": "rappdirs", + "Version": "0.3.3", + "Source": "Repository" + }, + "readr": { + "Package": "readr", + "Version": "2.1.5", + "Source": "Repository" + }, + "readxl": { + "Package": "readxl", + "Version": "1.4.3", + "Source": "Repository" + }, + "rematch": { + "Package": "rematch", + "Version": "2.0.0", + "Source": "Repository" + }, + "rematch2": { + "Package": "rematch2", + "Version": "2.1.2", + "Source": "Repository" + }, + "renv": { + "Package": "renv", + "Version": "1.0.7", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "utils" + ], + "Hash": "397b7b2a265bc5a7a06852524dabae20" + }, + "reprex": { + "Package": "reprex", + "Version": "2.1.0", + "Source": "Repository" + }, + "reshape2": { + "Package": "reshape2", + "Version": "1.4.4", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "Rcpp", + "plyr", + "stringr" + ], + "Hash": "bb5996d0bd962d214a11140d77589917" + }, + "reticulate": { + "Package": "reticulate", + "Version": "1.36.1", + "Source": "Repository" + }, + "rhdf5": { + "Package": "rhdf5", + "Version": "2.46.1", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "R", + "Rhdf5lib", + "S4Vectors", + "methods", + "rhdf5filters" + ], + "Hash": "b0a244022c3427cd8213c33804c6b5de" + }, + "rhdf5filters": { + "Package": "rhdf5filters", + "Version": "1.14.1", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.18", + "Requirements": [ + "Rhdf5lib" + ], + "Hash": "d27a2f6a89def6388fad5b0aae026220" + }, + "rlang": { + "Package": "rlang", + "Version": "1.1.3", + "Source": "Repository" + }, + "rmarkdown": { + "Package": "rmarkdown", + "Version": "2.26", + "Source": "Repository" + }, + "rprojroot": { + "Package": "rprojroot", + "Version": "2.0.4", + "Source": "Repository" + }, + "rstudioapi": { + "Package": "rstudioapi", + "Version": "0.16.0", + "Source": "Repository" + }, + "rvest": { + "Package": "rvest", + "Version": "1.0.4", + "Source": "Repository" + }, + "sass": { + "Package": "sass", + "Version": "0.4.9", + "Source": "Repository" + }, + "scales": { + "Package": "scales", + "Version": "1.3.0", + "Source": "Repository" + }, + "scuttle": { + "Package": "scuttle", + "Version": "1.12.0", + "Source": "Bioconductor", + "Requirements": [ + "BiocGenerics", + "BiocParallel", + "DelayedArray", + "DelayedMatrixStats", + "GenomicRanges", + "Matrix", + "Rcpp", + "S4Vectors", + "SingleCellExperiment", + "SummarizedExperiment", + "beachmat", + "methods", + "stats", + "utils" + ], + "Hash": "1412c4b6dfd8de528e1101e493e66a02" + }, + "selectr": { + "Package": "selectr", + "Version": "0.4-2", + "Source": "Repository" + }, + "sitmo": { + "Package": "sitmo", + "Version": "2.0.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "Rcpp" + ], + "Hash": "c956d93f6768a9789edbc13072b70c78" + }, + "snow": { + "Package": "snow", + "Version": "0.4-4", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "utils" + ], + "Hash": "40b74690debd20c57d93d8c246b305d4" + }, + "sparseMatrixStats": { + "Package": "sparseMatrixStats", + "Version": "1.14.0", + "Source": "Bioconductor", + "Requirements": [ + "Matrix", + "MatrixGenerics", + "Rcpp", + "matrixStats", + "methods" + ], + "Hash": "49383d0f6c6152ff7cb594f254c23cc8" + }, + "splines": { + "Package": "splines", + "Version": "4.3.3", + "Source": "R" + }, + "statmod": { + "Package": "statmod", + "Version": "1.5.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "graphics", + "stats" + ], + "Hash": "26e158d12052c279bdd4ba858b80fb1f" + }, + "stats": { + "Package": "stats", + "Version": "4.3.3", + "Source": "R" + }, + "stats4": { + "Package": "stats4", + "Version": "4.3.3", + "Source": "R" + }, + "stringi": { + "Package": "stringi", + "Version": "1.8.3", + "Source": "Repository" + }, + "stringr": { + "Package": "stringr", + "Version": "1.5.1", + "Source": "Repository" + }, + "svMisc": { + "Package": "svMisc", + "Version": "1.2.3", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "methods", + "stats", + "tools", + "utils" + ], + "Hash": "b13f5680860f67c32ccb006ad38f24f4" + }, + "sys": { + "Package": "sys", + "Version": "3.4.2", + "Source": "Repository" + }, + "systemfonts": { + "Package": "systemfonts", + "Version": "1.0.6", + "Source": "Repository" + }, + "textshaping": { + "Package": "textshaping", + "Version": "0.3.7", + "Source": "Repository" + }, + "tibble": { + "Package": "tibble", + "Version": "3.2.1", + "Source": "Repository" + }, + "tidyr": { + "Package": "tidyr", + "Version": "1.3.1", + "Source": "Repository" + }, + "tidyselect": { + "Package": "tidyselect", + "Version": "1.2.1", + "Source": "Repository" + }, + "tidyverse": { + "Package": "tidyverse", + "Version": "2.0.0", + "Source": "Repository" + }, + "timechange": { + "Package": "timechange", + "Version": "0.3.0", + "Source": "Repository" + }, + "tinytex": { + "Package": "tinytex", + "Version": "0.50", + "Source": "Repository" + }, + "tools": { + "Package": "tools", + "Version": "4.3.3", + "Source": "R" + }, + "tximport": { + "Package": "tximport", + "Version": "1.30.0", + "Source": "Bioconductor", + "Requirements": [ + "methods", + "stats", + "utils" + ], + "Hash": "6e9621b0f1bf9398255f32c7000a7e16" + }, + "tzdb": { + "Package": "tzdb", + "Version": "0.4.0", + "Source": "Repository" + }, + "utf8": { + "Package": "utf8", + "Version": "1.2.4", + "Source": "Repository" + }, + "utils": { + "Package": "utils", + "Version": "4.3.3", + "Source": "R" + }, + "uuid": { + "Package": "uuid", + "Version": "1.2-0", + "Source": "Repository" + }, + "vctrs": { + "Package": "vctrs", + "Version": "0.6.5", + "Source": "Repository" + }, + "viridisLite": { + "Package": "viridisLite", + "Version": "0.4.2", + "Source": "Repository" + }, + "vroom": { + "Package": "vroom", + "Version": "1.6.5", + "Source": "Repository" + }, + "withr": { + "Package": "withr", + "Version": "3.0.0", + "Source": "Repository" + }, + "xfun": { + "Package": "xfun", + "Version": "0.43", + "Source": "Repository" + }, + "xml2": { + "Package": "xml2", + "Version": "1.3.6", + "Source": "Repository" + }, + "yaml": { + "Package": "yaml", + "Version": "2.3.8", + "Source": "Repository" + }, + "zellkonverter": { + "Package": "zellkonverter", + "Version": "1.12.1", + "Source": "Repository" + }, + "zlibbioc": { + "Package": "zlibbioc", + "Version": "1.48.2", + "Source": "Repository" + } + } +} diff --git a/docker/requirements.in b/docker/requirements.in new file mode 100644 index 00000000..5bf61cd0 --- /dev/null +++ b/docker/requirements.in @@ -0,0 +1,8 @@ +anndata~=0.10 +etils<1.8 # v1.8 drops python 3.10 support +jax[cpu] +pandas +scanpy~=1.10 +scvi-tools~=1.1 +torch +torchvision diff --git a/docker/requirements.txt b/docker/requirements.txt index 86a4b11b..f8b1ee3c 100644 --- a/docker/requirements.txt +++ b/docker/requirements.txt @@ -1,151 +1,97 @@ -absl-py==1.4.0 -aiohttp==3.9.0 +# +# This file is autogenerated by pip-compile with Python 3.10 +# by the following command: +# +# pip-compile --no-annotate --output-file=requirements.txt --strip-extras requirements.in +# +absl-py==2.1.0 +aiohttp==3.9.5 aiosignal==1.3.1 -anndata==0.9.1 -annotated-types==0.5.0 -anyio==3.7.1 -arrow==1.2.3 -astunparse==1.6.3 -async-timeout==4.0.2 -attrs==23.1.0 -backoff==2.2.1 -beautifulsoup4==4.12.2 -blessed==1.20.0 -cached-property==1.5.2 -cachetools==5.3.0 -certifi==2023.7.22 -charset-normalizer==3.1.0 -chex==0.1.7 -click==8.1.6 +anndata==0.10.7 +array-api-compat==1.6 +async-timeout==4.0.3 +attrs==23.2.0 +chex==0.1.86 contextlib2==21.6.0 -contourpy==1.0.7 -croniter==1.4.1 -cycler==0.11.0 -dateutils==0.6.12 -deepdiff==6.3.1 -dm-tree==0.1.8 +contourpy==1.2.1 +cycler==0.12.1 docrep==0.3.2 -et-xmlfile==1.1.0 -etils==1.2.0 -exceptiongroup==1.1.3 -fastapi==0.101.1 -filelock==3.12.0 -flatbuffers==23.3.3 -flax==0.6.9 -fonttools==4.39.3 -frozenlist==1.3.3 -fsspec==2023.4.0 -gast==0.4.0 -google-auth==2.17.3 -google-auth-oauthlib==1.0.0 -google-pasta==0.2.0 -grpcio==1.54.0 -h11==0.14.0 -h5py==3.8.0 -idna==3.4 -importlib-metadata==6.6.0 -importlib-resources==5.12.0 -inquirer==3.1.3 -itsdangerous==2.1.2 -jax==0.4.8 -jaxlib==0.4.7 -Jinja2==3.1.2 -joblib==1.2.0 -keras==2.12.0 -kiwisolver==1.4.4 -libclang==16.0.0 -lightning==2.0.7 -lightning-cloud==0.5.37 -lightning-utilities==0.8.0 -llvmlite==0.40.1 -Markdown==3.4.3 -markdown-it-py==2.2.0 -MarkupSafe==2.1.2 -matplotlib==3.7.1 +etils==1.7.0 +exceptiongroup==1.2.0 +filelock==3.13.4 +flax==0.8.2 +fonttools==4.51.0 +frozenlist==1.4.1 +fsspec==2024.3.1 +h5py==3.11.0 +idna==3.7 +importlib-resources==6.4.0 +jax==0.4.26 +jaxlib==0.4.26 +jinja2==3.1.3 +joblib==1.4.0 +kiwisolver==1.4.5 +legacy-api-wrap==1.4 +lightning==2.1.4 +lightning-utilities==0.11.2 +llvmlite==0.42.0 +markdown-it-py==3.0.0 +markupsafe==2.1.5 +matplotlib==3.8.4 mdurl==0.1.2 ml-collections==0.1.1 -ml-dtypes==0.1.0 +ml-dtypes==0.4.0 mpmath==1.3.0 -msgpack==1.0.5 -mudata==0.2.2 -multidict==6.0.4 -multipledispatch==0.6.0 -natsort==8.3.1 -nest-asyncio==1.5.6 -networkx==3.1 -numba==0.57.1 -numpy==1.24.4 -numpyro==0.12.1 -oauthlib==3.2.2 -openpyxl==3.1.2 +msgpack==1.0.8 +mudata==0.2.3 +multidict==6.0.5 +multipledispatch==1.0.0 +natsort==8.4.0 +nest-asyncio==1.6.0 +networkx==3.3 +numba==0.59.1 +numpy==1.26.4 +numpyro==0.14.0 opt-einsum==3.3.0 -optax==0.1.5 -orbax-checkpoint==0.2.1 -ordered-set==4.1.0 -packaging==23.1 -pandas==2.0.1 -patsy==0.5.3 -Pillow==10.1.0 -protobuf==4.22.3 -psutil==5.9.5 -pyasn1==0.5.0 -pyasn1-modules==0.3.0 -pydantic==2.1.1 -pydantic_core==2.4.0 -Pygments==2.15.1 -PyJWT==2.8.0 -pynndescent==0.5.10 -pyparsing==3.0.9 +optax==0.2.2 +orbax-checkpoint==0.5.9 +packaging==24.0 +pandas==2.2.2 +patsy==0.5.6 +pillow==10.3.0 +protobuf==5.26.1 +pygments==2.17.2 +pynndescent==0.5.12 +pyparsing==3.1.2 pyro-api==0.1.2 -pyro-ppl==1.8.4 -python-dateutil==2.8.2 -python-editor==1.0.4 -python-multipart==0.0.6 -pytorch-lightning==2.0.7 -pytz==2023.3 -PyYAML==6.0 -readchar==4.0.5 -requests==2.31.0 -requests-oauthlib==1.3.1 -rich==13.3.5 -rsa==4.9 -scanpy==1.9.3 -scikit-learn==1.3.0 -scipy==1.11.1 -scvi-tools==1.0.3 -seaborn==0.12.2 +pyro-ppl==1.9.0 +python-dateutil==2.9.0.post0 +pytorch-lightning==2.2.2 +pytz==2024.1 +pyyaml==6.0.1 +rich==13.7.1 +scanpy==1.10.1 +scikit-learn==1.4.2 +scipy==1.13.0 +scvi-tools==1.1.2 +seaborn==0.13.2 session-info==1.0.0 six==1.16.0 -sniffio==1.3.0 -soupsieve==2.4.1 -sparse==0.14.0 -starlette==0.27.0 -starsessions==1.3.0 -statsmodels==0.14.0rc0 -stdlib-list==0.8.0 -sympy==1.11.1 -tensorboard==2.12.2 -tensorboard-data-server==0.7.0 -tensorboard-plugin-wit==1.8.1 -tensorflow-estimator==2.12.0 -tensorstore==0.1.36 -termcolor==2.3.0 -threadpoolctl==3.1.0 -toolz==0.12.0 -torch==2.0.1 -torchmetrics==0.11.4 -tqdm==4.65.0 -traitlets==5.9.0 -typing_extensions==4.7.1 -tzdata==2023.3 -umap-learn==0.5.3 -urllib3==2.1.0 -uvicorn==0.23.2 -wcwidth==0.2.6 -websocket-client==1.6.1 -websockets==11.0.3 -Werkzeug==3.0.1 -wrapt==1.14.1 -xarray==2023.7.0 -yarl==1.9.2 -zipp==3.15.0 +statsmodels==0.14.2 +stdlib-list==0.10.0 +sympy==1.12 +tensorstore==0.1.56 +threadpoolctl==3.4.0 +toolz==0.12.1 +torch==2.2.2 +torchmetrics==1.3.2 +torchvision==0.17.2 +tqdm==4.66.2 +typing-extensions==4.11.0 +tzdata==2024.1 +umap-learn==0.5.6 +yarl==1.9.4 +zipp==3.18.1 + +# The following packages are considered to be unsafe in a requirements file: +# setuptools diff --git a/docker/requirements_anndata.in b/docker/requirements_anndata.in new file mode 100644 index 00000000..c90c929e --- /dev/null +++ b/docker/requirements_anndata.in @@ -0,0 +1,2 @@ +# requirements.in packages for minimal ScPCA workflows +anndata~=0.10 diff --git a/docker/requirements_anndata.txt b/docker/requirements_anndata.txt new file mode 100644 index 00000000..071e9357 --- /dev/null +++ b/docker/requirements_anndata.txt @@ -0,0 +1,19 @@ +# +# This file is autogenerated by pip-compile with Python 3.10 +# by the following command: +# +# pip-compile --no-annotate --output-file=requirements_anndata.txt --strip-extras requirements_anndata.in +# +anndata==0.10.7 +array-api-compat==1.6 +exceptiongroup==1.2.1 +h5py==3.11.0 +natsort==8.4.0 +numpy==1.26.4 +packaging==24.0 +pandas==2.2.2 +python-dateutil==2.9.0.post0 +pytz==2024.1 +scipy==1.13.0 +six==1.16.0 +tzdata==2024.1 diff --git a/docker/requirements_scvi.in b/docker/requirements_scvi.in new file mode 100644 index 00000000..47067d40 --- /dev/null +++ b/docker/requirements_scvi.in @@ -0,0 +1,4 @@ +# requirements.in packages for scvi-based analysis +anndata~=0.10 +scanpy~=1.10 +scvi-tools~=1.1 diff --git a/docker/requirements_scvi.txt b/docker/requirements_scvi.txt new file mode 100644 index 00000000..cb1359cb --- /dev/null +++ b/docker/requirements_scvi.txt @@ -0,0 +1,96 @@ +# +# This file is autogenerated by pip-compile with Python 3.10 +# by the following command: +# +# pip-compile --no-annotate --output-file=requirements_scvi.txt --strip-extras requirements_scvi.in +# +absl-py==2.1.0 +aiohttp==3.9.5 +aiosignal==1.3.1 +anndata==0.10.7 +array-api-compat==1.6 +async-timeout==4.0.3 +attrs==23.2.0 +chex==0.1.86 +contextlib2==21.6.0 +contourpy==1.2.1 +cycler==0.12.1 +docrep==0.3.2 +etils==1.7.0 +exceptiongroup==1.2.1 +filelock==3.13.4 +flax==0.8.2 +fonttools==4.51.0 +frozenlist==1.4.1 +fsspec==2024.3.1 +h5py==3.11.0 +idna==3.7 +importlib-resources==6.4.0 +jax==0.4.26 +jaxlib==0.4.26 +jinja2==3.1.3 +joblib==1.4.0 +kiwisolver==1.4.5 +legacy-api-wrap==1.4 +lightning==2.1.4 +lightning-utilities==0.11.2 +llvmlite==0.42.0 +markdown-it-py==3.0.0 +markupsafe==2.1.5 +matplotlib==3.8.4 +mdurl==0.1.2 +ml-collections==0.1.1 +ml-dtypes==0.4.0 +mpmath==1.3.0 +msgpack==1.0.8 +mudata==0.2.3 +multidict==6.0.5 +multipledispatch==1.0.0 +natsort==8.4.0 +nest-asyncio==1.6.0 +networkx==3.3 +numba==0.59.1 +numpy==1.26.4 +numpyro==0.14.0 +opt-einsum==3.3.0 +optax==0.2.2 +orbax-checkpoint==0.5.10 +packaging==24.0 +pandas==2.2.2 +patsy==0.5.6 +pillow==10.3.0 +protobuf==5.26.1 +pygments==2.17.2 +pynndescent==0.5.12 +pyparsing==3.1.2 +pyro-api==0.1.2 +pyro-ppl==1.9.0 +python-dateutil==2.9.0.post0 +pytorch-lightning==2.2.2 +pytz==2024.1 +pyyaml==6.0.1 +rich==13.7.1 +scanpy==1.10.1 +scikit-learn==1.4.2 +scipy==1.13.0 +scvi-tools==1.1.2 +seaborn==0.13.2 +session-info==1.0.0 +six==1.16.0 +statsmodels==0.14.2 +stdlib-list==0.10.0 +sympy==1.12 +tensorstore==0.1.56 +threadpoolctl==3.4.0 +toolz==0.12.1 +torch==2.2.2 +torchmetrics==1.3.2 +tqdm==4.66.2 +typing-extensions==4.11.0 +tzdata==2024.1 +umap-learn==0.5.6 +yarl==1.9.4 +zipp==3.18.1 + +# The following packages are considered to be unsafe in a requirements file: +# setuptools diff --git a/docker/scpcatools_anndata.Dockerfile b/docker/scpcatools_anndata.Dockerfile new file mode 100644 index 00000000..fbb14f23 --- /dev/null +++ b/docker/scpcatools_anndata.Dockerfile @@ -0,0 +1,37 @@ +FROM bioconductor/r-ver:3.18 +LABEL maintainer="ccdl@alexslemonade.org" +LABEL org.opencontainers.image.source https://github.com/AlexsLemonade/scpcaTools +LABEL org.opencontainers.image.title "scpcatools-anndata" + +#### R packages +# Use renv for R packages +ENV RENV_CONFIG_CACHE_ENABLED FALSE +RUN Rscript -e "install.packages(c('remotes', 'renv'))" + +WORKDIR /usr/local/renv +COPY renv_zellkonverter.lock renv.lock +# restore renv and remove cache files +RUN Rscript -e "renv::restore()" && \ + rm -rf ~/.cache/R/renv && \ + rm -rf /tmp/downloaded_packages && \ + rm -rf /tmp/Rtmp* + +# Complete installation of zellkonverter conda env +ENV BASILISK_EXTERNAL_DIR /usr/local/renv/basilisk +RUN Rscript -e "proc <- basilisk::basiliskStart(env = zellkonverter::zellkonverterAnnDataEnv(), testload = 'anndata'); \ + basilisk::basiliskStop(proc); \ + basilisk.utils::cleanConda()" + +#### Python packages +COPY requirements_anndata.txt requirements.txt +RUN pip install --no-cache-dir -r requirements.txt + +########################## +# bust cache if needed +ADD "https://api.github.com/repos/AlexsLemonade/scpcaTools/commits?per_page=1" latest_commit +# Install scpcaTools package (& test loading) +RUN Rscript -e "remotes::install_github('AlexsLemonade/scpcaTools', upgrade = 'never'); \ + require(scpcaTools)" + +# set final workdir for commands +WORKDIR /home diff --git a/docker/scpcatools_reports.Dockerfile b/docker/scpcatools_reports.Dockerfile new file mode 100644 index 00000000..1e89f968 --- /dev/null +++ b/docker/scpcatools_reports.Dockerfile @@ -0,0 +1,27 @@ +FROM bioconductor/r-ver:3.18 +LABEL maintainer="ccdl@alexslemonade.org" +LABEL org.opencontainers.image.source https://github.com/AlexsLemonade/scpcaTools +LABEL org.opencontainers.image.title "scpcatools-slim" + +#### R packages +# Use renv for R packages +ENV RENV_CONFIG_CACHE_ENABLED FALSE +RUN Rscript -e "install.packages(c('remotes', 'renv'))" + +WORKDIR /usr/local/renv +COPY renv_reports.lock renv.lock +# restore renv and remove cache files +RUN Rscript -e "renv::restore()" && \ + rm -rf ~/.cache/R/renv && \ + rm -rf /tmp/downloaded_packages && \ + rm -rf /tmp/Rtmp* + +########################## +# bust cache if needed +ADD "https://api.github.com/repos/AlexsLemonade/scpcaTools/commits?per_page=1" latest_commit +# Install scpcaTools package (& test loading) +RUN Rscript -e "remotes::install_github('AlexsLemonade/scpcaTools', upgrade = 'never'); \ + require(scpcaTools)" + +# set final workdir for commands +WORKDIR /home diff --git a/docker/scpcatools_scvi.Dockerfile b/docker/scpcatools_scvi.Dockerfile new file mode 100644 index 00000000..e82aaa9c --- /dev/null +++ b/docker/scpcatools_scvi.Dockerfile @@ -0,0 +1,37 @@ +FROM bioconductor/r-ver:3.18 +LABEL maintainer="ccdl@alexslemonade.org" +LABEL org.opencontainers.image.source https://github.com/AlexsLemonade/scpcaTools +LABEL org.opencontainers.image.title "scpcatools-anndata" + +#### R packages +# Use renv for R packages +ENV RENV_CONFIG_CACHE_ENABLED FALSE +RUN Rscript -e "install.packages(c('remotes', 'renv'))" + +WORKDIR /usr/local/renv +COPY renv_zellkonverter.lock renv.lock +# restore renv and remove cache files +RUN Rscript -e "renv::restore()" && \ + rm -rf ~/.cache/R/renv && \ + rm -rf /tmp/downloaded_packages && \ + rm -rf /tmp/Rtmp* + +# Complete installation of zellkonverter conda env +ENV BASILISK_EXTERNAL_DIR /usr/local/renv/basilisk +RUN Rscript -e "proc <- basilisk::basiliskStart(env = zellkonverter::zellkonverterAnnDataEnv(), testload = 'anndata'); \ + basilisk::basiliskStop(proc); \ + basilisk.utils::cleanConda()" + +#### Python packages +COPY requirements_scvi.txt requirements.txt +RUN pip install --no-cache-dir -r requirements.txt + +########################## +# bust cache if needed +ADD "https://api.github.com/repos/AlexsLemonade/scpcaTools/commits?per_page=1" latest_commit +# Install scpcaTools package (& test loading) +RUN Rscript -e "remotes::install_github('AlexsLemonade/scpcaTools', upgrade = 'never'); \ + require(scpcaTools)" + +# set final workdir for commands +WORKDIR /home diff --git a/docker/scpcatools_seurat.Dockerfile b/docker/scpcatools_seurat.Dockerfile new file mode 100644 index 00000000..da967bca --- /dev/null +++ b/docker/scpcatools_seurat.Dockerfile @@ -0,0 +1,27 @@ +FROM bioconductor/r-ver:3.18 +LABEL maintainer="ccdl@alexslemonade.org" +LABEL org.opencontainers.image.source https://github.com/AlexsLemonade/scpcaTools +LABEL org.opencontainers.image.title "scpcatools-slim" + +#### R packages +# Use renv for R packages +ENV RENV_CONFIG_CACHE_ENABLED FALSE +RUN Rscript -e "install.packages(c('remotes', 'renv'))" + +WORKDIR /usr/local/renv +COPY renv_seurat.lock renv.lock +# restore renv and remove cache files +RUN Rscript -e "renv::restore()" && \ + rm -rf ~/.cache/R/renv && \ + rm -rf /tmp/downloaded_packages && \ + rm -rf /tmp/Rtmp* + +########################## +# bust cache if needed +ADD "https://api.github.com/repos/AlexsLemonade/scpcaTools/commits?per_page=1" latest_commit +# Install scpcaTools package (& test loading) +RUN Rscript -e "remotes::install_github('AlexsLemonade/scpcaTools', upgrade = 'never'); \ + require(scpcaTools)" + +# set final workdir for commands +WORKDIR /home diff --git a/docker/scpcatools_slim.Dockerfile b/docker/scpcatools_slim.Dockerfile new file mode 100644 index 00000000..8883a22e --- /dev/null +++ b/docker/scpcatools_slim.Dockerfile @@ -0,0 +1,27 @@ +FROM bioconductor/r-ver:3.18 +LABEL maintainer="ccdl@alexslemonade.org" +LABEL org.opencontainers.image.source https://github.com/AlexsLemonade/scpcaTools +LABEL org.opencontainers.image.title "scpcatools-slim" + +#### R packages +# Use renv for R packages +ENV RENV_CONFIG_CACHE_ENABLED FALSE +RUN Rscript -e "install.packages(c('remotes', 'renv'))" + +WORKDIR /usr/local/renv +COPY renv_slim.lock renv.lock +# restore renv and remove cache files +RUN Rscript -e "renv::restore()" && \ + rm -rf ~/.cache/R/renv && \ + rm -rf /tmp/downloaded_packages && \ + rm -rf /tmp/Rtmp* + +########################## +# bust cache if needed +ADD "https://api.github.com/repos/AlexsLemonade/scpcaTools/commits?per_page=1" latest_commit +# Install scpcaTools package (& test loading) +RUN Rscript -e "remotes::install_github('AlexsLemonade/scpcaTools', upgrade = 'never'); \ + require(scpcaTools)" + +# set final workdir for commands +WORKDIR /home diff --git a/docker/scripts/install_scpca_deps.sh b/docker/scripts/install_scpca_deps.sh index 7f367a24..c9bbb724 100644 --- a/docker/scripts/install_scpca_deps.sh +++ b/docker/scripts/install_scpca_deps.sh @@ -31,4 +31,6 @@ apt-get -y --no-install-recommends install \ pandoc \ python3-pip +apt-get clean + rm -rf /var/lib/apt/lists/* diff --git a/docker/scripts/make-lockfile.R b/docker/scripts/make-lockfile.R new file mode 100644 index 00000000..5d27f1d6 --- /dev/null +++ b/docker/scripts/make-lockfile.R @@ -0,0 +1,60 @@ +#!/usr/bin/env Rscript + +# This script is used to create or update a lockfile based on the current renv environment, +# including scpcaTools dependencies and any additional packages specified by the user. +# This means that it does _not_ look at what files are used by scripts in the project, except +# for the package DESCRIPTION file. +# The main `renv.lock` file is not updated by this script, but must be up to date with the +# current environment before running this script. + +library(optparse) + +option_list <- list( + make_option( + c("-f", "--lockfile"), + type = "character", + default = NULL, + help = "The lockfile to create." + ), + make_option( + c("-p", "--packages"), + type = "character", + default = "", + help = paste( + "Additional packages to include in the lockfile beyond scpcaTools requirements.", + "Comma, semicolon, or space separated." + ) + ) +) + +opts <- parse_args(OptionParser(option_list = option_list)) + +# change to project root to get renv (renv::load does not set bioc mirrors) +current_dir <- getwd() +setwd(here::here()) +source(".Rprofile") +setwd(current_dir) + +# Check that lockfile is up to date with currently installed packages +if (!renv::status()$synchronized) { + stop(paste( + "renv.lock file does not match installed packages.", + "Please run `renv::restore()` or `renv::snapshot()` from within R before running this script." + )) +} + +# get dependencies of scpcaTools +renv::snapshot(lockfile = opts$lockfile, type = "explicit") + +# additional dependencies for added packages +added_packages <- opts$packages |> + stringr::str_split_1("[,;\\s]+") |> + stringr::str_subset(".+") |> # remove empty strings + c("optparse", "scater", "scran", "tidyverse") # always include these +all_packages <- added_packages |> + tools::package_dependencies(recursive = TRUE) |> + unlist() |> + unique() |> + c(added_packages) + +renv::record(all_packages, lockfile = opts$lockfile) diff --git a/inst/WORDLIST b/inst/WORDLIST index e71f36ae..b8a39257 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -10,6 +10,8 @@ CMD colData coldata commenter +conda +dev Dockerfile DropletUtils emptyDrops @@ -33,6 +35,7 @@ ScPCA scpca scpcaData scpcaTools +scpcatools SingleCellExperiment Spielman tidyverse diff --git a/requirements.txt b/requirements.txt deleted file mode 120000 index be481796..00000000 --- a/requirements.txt +++ /dev/null @@ -1 +0,0 @@ -docker/requirements.txt \ No newline at end of file