Repositories list

• scxa-workflows

  Public
  Higher level repo for aggregating all of Atlas workflow logic for Single Cell

  Shell

  •

  Apache License 2.0

  •2•14•5•2•Updated Dec 4, 2024Dec 4, 2024

• scxa-tertiary-workflow

  Public
  Tertiary component for SCXA workflows

  Nextflow

  •0•0•0•1•Updated Dec 4, 2024Dec 4, 2024

• scxa-bundle-workflow

  Public
  Workflow for making bundles for Single-cell Expression Atlas

  Nextflow

  •0•0•1•1•Updated Dec 4, 2024Dec 4, 2024

• scxa-control-workflow

  Public
  Master Nextflow workflow for running each component of the SMART-seq and droplet SCXA pipelines

  R

  •2•4•4•1•Updated Dec 4, 2024Dec 4, 2024

• atlas-web-single-cell

  Public
  Single Cell Expression Atlas web application

  Java

  •

  Apache License 2.0

  •5•5•79•7•Updated Dec 4, 2024Dec 4, 2024

• scanpy-scripts

  Public
  Scripts for using scanpy

  Python

  •

  Apache License 2.0

  •13•31•11•4•Updated Dec 3, 2024Dec 3, 2024

• atlas-components

  Public
  Front end components of Expression Atlas and Single Cell Expression Atlas

  JavaScript

  •3•3•15•2•Updated Dec 3, 2024Dec 3, 2024

• atlas-web-bulk

  Public
  Bulk Expression Atlas web application

  Java

  •

  Apache License 2.0

  •1•0•38•5•Updated Dec 2, 2024Dec 2, 2024

• container-galaxy-sc-tertiary

  Public
  Galaxy container for single cell RNA-Seq tertiary analysis tools

  Python

  •

  MIT License

  •14•16•26•13•Updated Dec 1, 2024Dec 1, 2024

• atlas-release-notes

  Public
  Release notes for (Single Cell) Expression Atlas

  Shell

  •0•0•1•2•Updated Nov 27, 2024Nov 27, 2024

• atlas-bulk-baseline-ot-export-wf

  Public
  New baseline export for Open Targets (although it is meant as a general purpose export)

  Python

  •0•0•0•0•Updated Nov 27, 2024Nov 27, 2024

• index-bioentities

  Public
  Scripts to automate building and populating the bioentities collection

  Shell

  •0•0•0•1•Updated Nov 22, 2024Nov 22, 2024

• atlas-web-core

  Public
  Business logic for single cell and bulk Expression Atlas and for the up-and-coming Expression Atlas API

  Java

  •1•0•4•0•Updated Nov 22, 2024Nov 22, 2024

• submissions-tracking-interface

  Public
  An interface for browsing the ArrayExpress submissions tracking database

  HTML

  •0•0•0•0•Updated Nov 19, 2024Nov 19, 2024

• curated-metadata

  Public
  Relevant curated metadata to be consumed by Atlas Prod pipelines and Atlas Web Applications

  Python

  •0•2•0•0•Updated Nov 15, 2024Nov 15, 2024

• galaxy-gxa-tools-setup

  Public
  Standard tool installation for GXA Galaxy instances

  Python

  •2•0•0•0•Updated Nov 9, 2024Nov 9, 2024

• experiments-summary-panel

  Public
  Experiments panel for bulk Expression Atlas and Single Cell Expression Atlas

  JavaScript

  •0•0•0•0•Updated Nov 7, 2024Nov 7, 2024

• species-summary-panel

  Public
  Species panel for bulk Expression Atlas and Single Cell Expression Atlas

  JavaScript

  •0•0•0•0•Updated Nov 7, 2024Nov 7, 2024

• scxa-aggregation-workflow

  Public
  Aggregation component for SCXA workflows

  Nextflow

  •1•0•0•1•Updated Nov 1, 2024Nov 1, 2024

• scxa-droplet-quantification-workflow

  Public
  Quantification component for droplet-based studies

  Nextflow

  •1•5•0•0•Updated Oct 25, 2024Oct 25, 2024

• scxa-smartseq-quantification-workflow

  Public
  The SCXA smart-seq quantification workflow

  Nextflow

  •1•0•0•0•Updated Oct 25, 2024Oct 25, 2024

• galaxy-workflow-executor

  Public
  Utility scripts to run a Galaxy workflow on Galaxy through the CLI

  Python

  •0•1•5•2•Updated Oct 24, 2024Oct 24, 2024

• atlas-annotations

  Public
  The pipeline producing bioentity annotations used in Expression Atlas searches

  Shell

  •1•0•10•6•Updated Oct 22, 2024Oct 22, 2024

• atlas-gtex-bulk

  Public
  Atlas analysis for controlled-access GTEx bulk datasets

  rna-seqgtex

  Python

  •0•0•3•1•Updated Oct 21, 2024Oct 21, 2024

• atlas-ca-analysis

  Public
  Atlas analysis for controlled-access bulk datasets, such as EGA

  Shell

  •

  Apache License 2.0

  •0•0•1•0•Updated Oct 15, 2024Oct 15, 2024

• db-scxa

  Public
  An AtlasProd module for loading scxa-analytics data to postgres.

  Shell

  •1•2•4•3•Updated Oct 8, 2024Oct 8, 2024

• release-notes-generator

  Public
  A helper project to generate release notes for our web apps

  Java

  •

  Apache License 2.0

  •0•0•3•0•Updated Oct 7, 2024Oct 7, 2024

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •3.3k•1•0•2•Updated Oct 7, 2024Oct 7, 2024

• perl-atlas-modules

  Public
  Repository of in-house atlas perl modules used for data production

  Perl

  •

  Apache License 2.0

  •1•0•1•7•Updated Oct 2, 2024Oct 2, 2024

• atlas-containers

  Public
  Common location to place our container definitions for integration with CI processes.

  Dockerfile

  •0•0•3•2•Updated Sep 20, 2024Sep 20, 2024