miBrain.yml

name: miBrain

channels:
  - conda-forge
  - bioconda

dependencies:
  - conda-forge::r-base==4.2.2
  - conda-forge::r-devtools
  - conda-forge::r-biocmanager
  - conda-forge::r-matrix
  - conda-forge::r-tidyverse
  - conda-forge::r-readxl
  - conda-forge::r-writexl
  - conda-forge::r-seriation
  - conda-forge::r-gridExtra
  ### R plotting
  - conda-forge::r-ggpubr
  - conda-forge::r-ggrastr
  - conda-forge::r-ggrepel
  - conda-forge::r-patchwork
  - conda-forge::r-cowplot
  - bioconda::bioconductor-complexheatmap
  ### python
  - conda-forge::pip
  - conda-forge::rpy2
  - conda-forge::numpy>=1.21.6
  - conda-forge::numba>=0.56.3
  - conda-forge::pandas>=1.5.0
  - conda-forge::python>=3.8
  - conda-forge::numpy_groupies>=0.9.15
  - conda-forge::requests>=2.25
  - bioconda::geosketch>=1.2
  - conda-forge::anndata>=0.8
  - conda-forge::scikit-learn>=1.2.2
  - conda-forge::tqdm>=4.3,<5.0
  - conda-forge::plotnine
  - conda-forge::biopython>=1.78
  - conda-forge::seaborn
  - conda-forge::umap-learn
  ### genomics
  - bioconda::bioconductor-rtracklayer
  - bioconda::bioconductor-genomicfeatures
  - bioconda::subread==1.6.2
  - bioconda::star==2.7.9a
  ### DEG
  - bioconda::bioconductor-deseq2
  - bioconda::bioconductor-limma
  - bioconda::bioconductor-edger
  ### GO
  - bioconda::bioconductor-go.db
  - bioconda::bioconductor-do.db
  - bioconda::bioconductor-org.hs.eg.db
  - bioconda::bioconductor-clusterprofiler
  ### jupyter
  - conda-forge::jupyterlab
  - conda-forge::nbconvert
  - conda-forge::r-irkernel
  - pip:
    - git+https://github.com/ventolab/CellphoneDB.git