Pinned Repositories
anatomogram
Anatomogram illustrating Expression Atlas experiments
atlas
Expression Atlas
atlas-heatmap
Heatmap visualizing bulk Expression Atlas data
container-galaxy-sc-tertiary
Galaxy container for single cell RNA-Seq tertiary analysis tools
monocle-scripts
Command line scripts wrapping functions in monocle3
r-seurat-scripts
Scripts to install as a Bioconda package for making workflows
react-ebi-species
scanpy-scripts
Scripts for using scanpy
scanpy-workflow
Workflow leveraging the scanpy-scripts package to run Scanpy in a Nextflow workflow
scxa-workflows
Higher level repo for aggregating all of Atlas workflow logic for Single Cell
EBI Gene Expression Group's Repositories
ebi-gene-expression-group/scanpy-scripts
Scripts for using scanpy
ebi-gene-expression-group/container-galaxy-sc-tertiary
Galaxy container for single cell RNA-Seq tertiary analysis tools
ebi-gene-expression-group/r-seurat-scripts
Scripts to install as a Bioconda package for making workflows
ebi-gene-expression-group/scxa-workflows
Higher level repo for aggregating all of Atlas workflow logic for Single Cell
ebi-gene-expression-group/atlas-web-single-cell
Single Cell Expression Atlas web application
ebi-gene-expression-group/scxa-droplet-quantification-workflow
Quantification component for droplet-based studies
ebi-gene-expression-group/scxa-control-workflow
Master Nextflow workflow for running each component of the SMART-seq and droplet SCXA pipelines
ebi-gene-expression-group/atlas-components
Front end components of Expression Atlas and Single Cell Expression Atlas
ebi-gene-expression-group/curated-metadata
Relevant curated metadata to be consumed by Atlas Prod pipelines and Atlas Web Applications
ebi-gene-expression-group/db-scxa
An AtlasProd module for loading scxa-analytics data to postgres.
ebi-gene-expression-group/atlas-conda
Internal conda recipes relevant for atlas but not of general interest to be in bioconda
ebi-gene-expression-group/atlas-web-bulk
Bulk Expression Atlas web application
ebi-gene-expression-group/galaxy-gxa-tools-setup
Standard tool installation for GXA Galaxy instances
ebi-gene-expression-group/galaxy-workflow-executor
Utility scripts to run a Galaxy workflow on Galaxy through the CLI
ebi-gene-expression-group/organ-anatomogram
ebi-gene-expression-group/atlas-anndata
Tools for anndata generation/ consumption for Expression Atlas
ebi-gene-expression-group/atlas-bash-util
ebi-gene-expression-group/atlas-bulk-baseline-ot-export-wf
New baseline export for Open Targets (although it is meant as a general purpose export)
ebi-gene-expression-group/atlas-containers
Common location to place our container definitions for integration with CI processes.
ebi-gene-expression-group/atlas-fastq-provider
Scripts and utilities for providing fastqs to workflows
ebi-gene-expression-group/atlas-gene-annotation-manipulation
Scripts for processing gene (or exon/ transcript) annotation
ebi-gene-expression-group/atlas-release-notes
Release notes for (Single Cell) Expression Atlas
ebi-gene-expression-group/atlas-web-core
Business logic for single cell and bulk Expression Atlas and for the up-and-coming Expression Atlas API
ebi-gene-expression-group/data-exports-bulk
Data export module for Atlas Prod
ebi-gene-expression-group/experiment_metadata
experiment_metadata code, factored out from atlas-prod
ebi-gene-expression-group/index-bioentities
Scripts to automate building and populating the bioentities collection
ebi-gene-expression-group/restful-notes-spring-hateoas-demo
Example project that uses springdata-rest-api-spec
ebi-gene-expression-group/scxa-aggregation-workflow
Aggregation component for SCXA workflows
ebi-gene-expression-group/scxa-bundle-workflow
Workflow for making bundles for Single-cell Expression Atlas
ebi-gene-expression-group/scxa-smartseq-quantification-workflow
The SCXA smart-seq quantification workflow