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@epigen

Bock Lab @ CeMM & Medical University of Vienna

Research and Software for Epigenetics, Bioinformatics & ML/AI, Single-cell Sequencing, Cancer Immunology, CRISPR Screening etc.

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  1. CellWhisperer CellWhisperer Public

    CellWhisperer bridges the gap between transcriptomics data and natural language, enabling intuitive interaction with scRNA-seq datasets

    Jupyter Notebook 199 26

  2. MrBiomics MrBiomics Public

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

    R 165 3

  3. atacseq_pipeline atacseq_pipeline Public

    Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.

    Python 99 2

  4. enrichment_analysis enrichment_analysis Public

    A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget and RcisTarget.

    Python 74 4

  5. unsupervised_analysis unsupervised_analysis Public

    A general purpose Snakemake workflow and MrBiomics module to perform unsupervised analyses (dimensionality reduction & cluster analysis) and visualizations of high-dimensional data.

    Python 65 4

  6. dea_limma dea_limma Public

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

    R 62 2

Repositories

Showing 10 of 48 repositories
  • enrichment_analysis Public

    A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget and RcisTarget.

    epigen/enrichment_analysis’s past year of commit activity
    Python 74 MIT 4 5 2 Updated Apr 5, 2026
  • unsupervised_analysis Public

    A general purpose Snakemake workflow and MrBiomics module to perform unsupervised analyses (dimensionality reduction & cluster analysis) and visualizations of high-dimensional data.

    epigen/unsupervised_analysis’s past year of commit activity
    Python 65 MIT 4 19 0 Updated Apr 1, 2026
  • MrBiomics Public

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

    epigen/MrBiomics’s past year of commit activity
    R 165 MIT 3 28 0 Updated Apr 1, 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.

    epigen/dea_limma’s past year of commit activity
    R 62 MIT 2 0 0 Updated Mar 24, 2026
  • RnBeads Public Forked from cirruswolke/RnBeads

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

    epigen/RnBeads’s past year of commit activity
    R 8 14 26 1 Updated Mar 16, 2026
  • CellWhisperer Public

    CellWhisperer bridges the gap between transcriptomics data and natural language, enabling intuitive interaction with scRNA-seq datasets

    epigen/CellWhisperer’s past year of commit activity
    Jupyter Notebook 199 GPL-3.0 26 3 0 Updated Mar 9, 2026
  • cellxgene Public

    Fork of `cellxgene` repository with adaptations for CellWhisperer and SpotWhisperer

    epigen/cellxgene’s past year of commit activity
    JavaScript 0 MIT 1 1 1 Updated Mar 5, 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 file format powered by the R package Seurat.

    epigen/scrnaseq_processing_seurat’s past year of commit activity
    R 58 MIT 3 4 0 Updated Jan 29, 2026
  • IgManalyser Public

    Code for the IgM array preprocessing and downstream analysis

    epigen/IgManalyser’s past year of commit activity
    R 0 MIT 0 0 0 Updated Jan 11, 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-generation sequencing (NGS) experiments (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including confounding factor analysis and diagnostic visualizations.

    epigen/spilterlize_integrate’s past year of commit activity
    R 53 MIT 3 1 0 Updated Jan 9, 2026
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