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/atlas-k8s-ci-environment
Collection of Kubernetes manifests for CI of Expression Atlas web applications
ebi-gene-expression-group/galaxy-workflow-executor
Utility scripts to run a Galaxy workflow on Galaxy through the CLI
ebi-gene-expression-group/geo-importer
Atlas Prod Importer for GEO
ebi-gene-expression-group/wf-bulk-indexing
Running logic for the indexing tasks for Bulk Expression Atlas
ebi-gene-expression-group/annotare-help
Help pages for functional genomics submissions
ebi-gene-expression-group/atlas-analysis
Scripts used in Atlas analysis pipelines
ebi-gene-expression-group/atlas-experiment
Experiment page for bulk Expression Atlas
ebi-gene-expression-group/atlas-gtex-bulk
Atlas analysis for controlled-access GTEx bulk datasets
ebi-gene-expression-group/bulk-recalculations
Snakemake workflow for new experiments processing, reprocessing and recalculations steps
ebi-gene-expression-group/expression-atlas-curation-guide
Curation rules and experiment inclusion criteria for the Expression Atlas
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-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-metadata-validator
Simple MAGE-TAB parser and validation rules for experiments loaded into (Single Cell) Expression Atlas
ebi-gene-expression-group/atlas-schemas
Schemas for the database and SolrCloud servers used by Expression Atlas and Single Cell Expression Atlas
ebi-gene-expression-group/data-exports-bulk
Data export module for Atlas Prod
ebi-gene-expression-group/experiments-summary-panel
Experiments panel for bulk Expression Atlas and Single Cell Expression Atlas
ebi-gene-expression-group/garnett-cli
Command line interface for the Garnett cell type classification tool
ebi-gene-expression-group/index-bioentities
Scripts to automate building and populating the bioentities collection
ebi-gene-expression-group/index-gxa
Repository that handles indexing of GXA studies.
ebi-gene-expression-group/index-scxa
Schema and loading methods for scxa-analytics index
ebi-gene-expression-group/restful-notes-spring-hateoas-demo
Example project that uses springdata-rest-api-spec
ebi-gene-expression-group/scmap-cli
CLI scripts for the scmap Bioconductor package
ebi-gene-expression-group/scpred-cli
Command-line interface for the scPred cell classifaction package
ebi-gene-expression-group/scxa-smartseq-quantification-workflow
The SCXA smart-seq quantification workflow
ebi-gene-expression-group/snRNA-mapping-rate
Comparison of Mapping rates for snRNA-Seq datasets with or without introns in reference and different mapping tools
ebi-gene-expression-group/solr-bulk
Scripts to create and manage Solr collections used by (bulk) Expression Atlas
ebi-gene-expression-group/solr-jsonl-loader
Script that partitions JSONL files and sends them to Solr
ebi-gene-expression-group/species-summary-panel
Species panel for bulk Expression Atlas and Single Cell Expression Atlas
ebi-gene-expression-group/submissions-biostudies-api
Web app to retrieve flat file information from the BioStudies API