Repositories list

• RnBeads

  Public
  Git working Repo synced to the Bioconductor: http://bioconductor.org/packages/devel/bioc/html/RnBeads.html

  R

  •1515 forks in epigen/RnBeads•99 stars in epigen/RnBeads•2626 issues in epigen/RnBeads•22 pull requests in epigen/RnBeads•Updated Oct 13, 2026Oct 13, 2026

• MrBiomics

  Public
  MrBiomics: Composable modules and recipes automate bioinformatics for multi-omics analyses

  pythonsciencerecipes+ 14

  pythonsciencerecipesdata-scienceautomationbioinformaticssnakemakeframeworkrresearch+ 7

  R

  •

  MIT License

  •33 forks in epigen/MrBiomics•177177 stars in epigen/MrBiomics•3838 issues in epigen/MrBiomics•00 pull requests in epigen/MrBiomics•Updated Aug 3, 2026Aug 3, 2026

• IgManalyser

  Public
  Code for the IgM array preprocessing and downstream analysis

  R

  •

  MIT License

  •00 forks in epigen/IgManalyser•00 stars in epigen/IgManalyser•00 issues in epigen/IgManalyser•00 pull requests in epigen/IgManalyser•Updated Apr 8, 2026Apr 8, 2026

• dea_limma

  Public
  A Snakemake workflow and MrBiomics module for performing and visualizing differential analyses of NGS data powered by the R package limma.

  visualizationworkflowbioinformatics+ 14

  visualizationworkflowbioinformaticsrna-seqsnakemakerstatisticsdeascrna-seqchip-seq+ 7

  R

  •

  MIT License

  •22 forks in epigen/dea_limma•6464 stars in epigen/dea_limma•00 issues in epigen/dea_limma•00 pull requests in epigen/dea_limma•Updated Mar 24, 2026Mar 24, 2026

• scrnaseq_processing_seurat

  Public
  A Snakemake workflow and MrBiomics module for processing and visualizing (multimodal) sc/snRNA-seq data generated with 10X Genomics Kits or in the MTX matrix fi…

  visualizationworkflowbioinformatics+ 8

  visualizationworkflowbioinformaticssnakemakescrna-seqsingle-cell10xgenomicsbiomedical-data-sciencecite-seqsnrna-seq+ 1

  R

  •

  MIT License

  •33 forks in epigen/scrnaseq_processing_seurat•6060 stars in epigen/scrnaseq_processing_seurat•44 issues in epigen/scrnaseq_processing_seurat•00 pull requests in epigen/scrnaseq_processing_seurat•Updated Jan 29, 2026Jan 29, 2026

• spilterlize_integrate

  Public
  A Snakemake workflow and MrBiomics module to split, filter, normalize, integrate and select highly variable features of count matrices resulting from next-gener…

  visualizationworkflowbioinformatics+ 13

  visualizationworkflowbioinformaticsrna-seqsnakemakeintegrationpipelinengsdimensionality-reductionchip-seq+ 6

  R

  •

  MIT License

  •33 forks in epigen/spilterlize_integrate•5454 stars in epigen/spilterlize_integrate•22 issues in epigen/spilterlize_integrate•00 pull requests in epigen/spilterlize_integrate•Updated Jan 9, 2026Jan 9, 2026

• mixscape_seurat

  Public
  A Snakemake workflow and MrBiomics module for performing perturbation analyses of pooled (multimodal) CRISPR screens with sc/snRNA-seq read-out (scCRISPR-seq) p…

  visualizationworkflowbioinformatics+ 7

  visualizationworkflowbioinformaticssnakemakescrna-seqsingle-cellbiomedical-data-scienceperturbation-analysissnrna-seqsccrispr-seq

  R

  •

  MIT License

  •22 forks in epigen/mixscape_seurat•5656 stars in epigen/mixscape_seurat•22 issues in epigen/mixscape_seurat•00 pull requests in epigen/mixscape_seurat•Updated Dec 7, 2025Dec 7, 2025

• dea_seurat

  Public
  A Snakemake workflow and MrBiomics module for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R package Seura…

  visualizationworkflowbioinformatics+ 7

  visualizationworkflowbioinformaticssnakemakescrna-seqsingle-cellbiomedical-data-sciencedifferential-expression-analysisvolcano-plotsnrna-seq

  R

  •

  MIT License

  •1111 forks in epigen/dea_seurat•5656 stars in epigen/dea_seurat•33 issues in epigen/dea_seurat•00 pull requests in epigen/dea_seurat•Updated Sep 5, 2025Sep 5, 2025

• ShinyCell2

  Public
  Fork of ShinyCell2 customised for SD/LDR HEACA Atlas.

  R

  •

  GNU General Public License v3.0

  •1919 forks in epigen/ShinyCell2•00 stars in epigen/ShinyCell2•00 issues in epigen/ShinyCell2•00 pull requests in epigen/ShinyCell2•Updated Aug 27, 2025Aug 27, 2025

• RnBeadsAnnotationCreator

  Public
  R

  •22 forks in epigen/RnBeadsAnnotationCreator•00 stars in epigen/RnBeadsAnnotationCreator•11 issue in epigen/RnBeadsAnnotationCreator•00 pull requests in epigen/RnBeadsAnnotationCreator•Updated Jun 22, 2022Jun 22, 2022

• Artemether_scRNA

  Public
  Single cell RNA-seq analysis of pancreatic islets with drug treatment

  R

  •11 fork in epigen/Artemether_scRNA•33 stars in epigen/Artemether_scRNA•00 issues in epigen/Artemether_scRNA•00 pull requests in epigen/Artemether_scRNA•Updated Mar 25, 2020Mar 25, 2020

• lch_hierarchy

  Public
  Code for Epigenomics and Single-cell Sequencing Define a Developmental Hierarchy in Langerhans Cell Histiocytosis (Halbritter, Farlik, et al. 2019 Cancer Discov…

  R

  •33 forks in epigen/lch_hierarchy•00 stars in epigen/lch_hierarchy•00 issues in epigen/lch_hierarchy•00 pull requests in epigen/lch_hierarchy•Updated Feb 3, 2020Feb 3, 2020

• cll-ibrutinib_time

  Public archive
  R

  •22 forks in epigen/cll-ibrutinib_time•22 stars in epigen/cll-ibrutinib_time•00 issues in epigen/cll-ibrutinib_time•00 pull requests in epigen/cll-ibrutinib_time•Updated Aug 13, 2019Aug 13, 2019

• GBMatch

  Public
  Code and metadata for glioblastoma matched analysis

  R

  •22 forks in epigen/GBMatch•1010 stars in epigen/GBMatch•00 issues in epigen/GBMatch•00 pull requests in epigen/GBMatch•Updated Jan 19, 2019Jan 19, 2019

• methylation-biomarker-benchmark

  Public
  Supplementary code repository accompanying the BLUEPRINT benchmark study of locus-specific DNA methylation assays.

  R

  •

  MIT License

  •00 forks in epigen/methylation-biomarker-benchmark•44 stars in epigen/methylation-biomarker-benchmark•00 issues in epigen/methylation-biomarker-benchmark•00 pull requests in epigen/methylation-biomarker-benchmark•Updated Jun 29, 2016Jun 29, 2016