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/anatomogram
Anatomogram illustrating Expression Atlas experiments
ebi-gene-expression-group/monocle-scripts
Command line scripts wrapping functions in monocle3
ebi-gene-expression-group/scxa-faceted-search-results
ebi-gene-expression-group/usi-arrayexpress
ArrayExpress USI metadata schemas and scripts for handling USI JSON metadata
ebi-gene-expression-group/atlas-cell-type-wheel
ebi-gene-expression-group/cell-types-eval-control-workflow
ebi-gene-expression-group/cell-types-eval-control-workflow-cross-validation
ebi-gene-expression-group/cell-types-eval-workflows
Higher-level repository containing individual workflows for evaluation of cell type prediction tools.
ebi-gene-expression-group/cell-types-prod-control-workflow
cell-types-prod-control-workflow
ebi-gene-expression-group/cell-types-prod-workflows
ebi-gene-expression-group/cellassign-cli
CellAssign is a marker-based cell type identification method.
ebi-gene-expression-group/common-datamodel
A data model describing the experimental metadata attributes that are used for converting other data formats to MAGE-TAB
ebi-gene-expression-group/eQTL-Catalogue-website
Get up and running with EBI-themed Jekyll fast (rolled with gh-pages in mind, clone/fork suggested)
ebi-gene-expression-group/garnett-eval-workflow
Nextflow pipeline for garnett-cli tool
ebi-gene-expression-group/garnett-prod-workflow
ebi-gene-expression-group/hello
Classic hello world script in Nextflow language
ebi-gene-expression-group/irap
integrated RNA-seq Analysis Pipeline
ebi-gene-expression-group/label-analysis-eval-workflow
Nextflow wrapper for predicted labels analysis component
ebi-gene-expression-group/nextflow
A DSL for data-driven computational pipelines
ebi-gene-expression-group/organ-anatomagram-celltype-heatmap
ebi-gene-expression-group/pypeln-feedstock
A conda-smithy repository for pypeln.
ebi-gene-expression-group/rnaseq
RNA sequencing analysis pipeline using STAR, HISAT2 and Salmon with gene counts and quality control
ebi-gene-expression-group/rnatoy
A proof of concept RNA-Seq pipeline with Nextflow
ebi-gene-expression-group/scmap-eval-workflow
Nextflow pipeline for the scmap tool
ebi-gene-expression-group/scmap-prod-workflow
ebi-gene-expression-group/scpred-eval-workflow
Nextflow pipeline for scpred package
ebi-gene-expression-group/scpred-prod-workflow
ebi-gene-expression-group/scran-cli
Command line interface for scran package. Low-level analyses of single-cell RNA-seq data.
ebi-gene-expression-group/scxa-plots
Repository for providing useful plots in Single-cell Expression Atlas workflows
ebi-gene-expression-group/tertiary_workflows_docs
Documentation associated with our project to generate tertiary workflow components for single-cell RNA-seq