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@ebi-gene-expression-group EBI Gene Expression Group

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    182 repositories

    • scxa-tertiary-workflow

      Public
      Tertiary component for SCXA workflows
      Nextflow
      •0•0•0•1•Updated Nov 4, 2024Nov 4, 2024

    • atlas-web-bulk

      Public
      Bulk Expression Atlas web application
      Java
      •
      Apache License 2.0
      •1•0•36•6•Updated Nov 4, 2024Nov 4, 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 4, 2024Nov 4, 2024

    • container-galaxy-sc-tertiary

      Public
      Galaxy container for single cell RNA-Seq tertiary analysis tools
      Python
      •
      MIT License
      •14•16•26•13•Updated Nov 1, 2024Nov 1, 2024

    • scxa-aggregation-workflow

      Public
      Aggregation component for SCXA workflows
      Nextflow
      •1•0•0•1•Updated Nov 1, 2024Nov 1, 2024

    • atlas-web-single-cell

      Public
      Single Cell Expression Atlas web application
      Java
      •
      Apache License 2.0
      •5•5•75•5•Updated Oct 31, 2024Oct 31, 2024

    • atlas-components

      Public
      Front end components of Expression Atlas and Single Cell Expression Atlas
      JavaScript
      •3•3•13•0•Updated Oct 30, 2024Oct 30, 2024

    • galaxy-gxa-tools-setup

      Public
      Standard tool installation for GXA Galaxy instances
      Python
      •2•0•0•0•Updated Oct 29, 2024Oct 29, 2024

    • scxa-workflows

      Public
      Higher level repo for aggregating all of Atlas workflow logic for Single Cell
      Shell
      •
      Apache License 2.0
      •2•14•5•1•Updated Oct 25, 2024Oct 25, 2024

    • scxa-bundle-workflow

      Public
      Workflow for making bundles for Single-cell Expression Atlas
      Nextflow
      •0•0•1•0•Updated Oct 25, 2024Oct 25, 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

    • scxa-control-workflow

      Public
      Master Nextflow workflow for running each component of the SMART-seq and droplet SCXA pipelines
      R
      •2•4•4•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

    • atlas-release-notes

      Public
      Release notes for (Single Cell) Expression Atlas
      Shell
      •0•0•1•2•Updated Sep 20, 2024Sep 20, 2024

    • r-seurat-scripts

      Public
      Scripts to install as a Bioconda package for making workflows
      R
      •
      Apache License 2.0
      •5•17•2•1•Updated Sep 15, 2024Sep 15, 2024

    • atlas-help-pages

      Public
      HTML
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Sep 4, 2024Sep 4, 2024

    • curated-metadata

      Public
      Relevant curated metadata to be consumed by Atlas Prod pipelines and Atlas Web Applications
      Python
      •0•2•0•0•Updated Aug 27, 2024Aug 27, 2024

    • scanpy-scripts

      Public
      Scripts for using scanpy
      Python
      •
      Apache License 2.0
      •13•31•11•4•Updated Aug 22, 2024Aug 22, 2024

    • atlas-bash-util

      Public
      Shell
      •0•0•2•1•Updated Aug 7, 2024Aug 7, 2024

    • atlas-deconvolution-references

      Public
      Generate single-cell reference dataset for deconvolution in Atlas
      R
      •
      Apache License 2.0
      •0•0•1•0•Updated Aug 2, 2024Aug 2, 2024

    • experiment_metadata

      Public
      experiment_metadata code, factored out from atlas-prod
      Shell
      •0•0•3•2•Updated Jul 30, 2024Jul 30, 2024