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@epigen

Computational Epigenetics

Computational Epigenetics Research and Software

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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 49 7

  2. MrBiomics MrBiomics Public

    MrBiomics: Modules & Recipes augment Bioinformatics for Multi-Omics Analyses

    Python 43 1

  3. atacseq_pipeline atacseq_pipeline Public

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

    Python 50 2

  4. KPNN KPNN Public

    Knowledge-primed neural networks

    Python 35 8

  5. 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 32 2

  6. crop-seq crop-seq Public archive

    Data analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)

    Python 30 13

Repositories

Showing 10 of 44 repositories
  • 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 7 12 23 0 Updated Jan 30, 2025
  • UCE Public Forked from snap-stanford/UCE

    UCE is a zero-shot foundation model for single-cell gene expression data

    epigen/UCE’s past year of commit activity
    Python 0 MIT 32 0 0 Updated Jan 30, 2025
  • cellxgene Public

    Bare clone of cellxgene

    epigen/cellxgene’s past year of commit activity
    JavaScript 0 MIT 0 0 1 Updated Jan 27, 2025
  • dea_limma Public

    A Snakemake workflow and MrBiomics module for performing and visualizing differential (expression) analyses (DEA) on NGS data powered by the R package limma.

    epigen/dea_limma’s past year of commit activity
    R 24 MIT 2 7 0 Updated Jan 23, 2025
  • scEval Public Forked from HelloWorldLTY/scEval

    Bock lab fork of scEval

    epigen/scEval’s past year of commit activity
    Jupyter Notebook 0 9 0 0 Updated Dec 28, 2024
  • MrBiomics Public

    MrBiomics: Modules & Recipes augment Bioinformatics for Multi-Omics Analyses

    epigen/MrBiomics’s past year of commit activity
    Python 43 MIT 1 20 0 Updated Dec 26, 2024
  • 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) powered by the R package Seurat's method Mixscape.

    epigen/mixscape_seurat’s past year of commit activity
    R 15 MIT 2 1 0 Updated Dec 20, 2024
  • 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 18 MIT 1 3 0 Updated Dec 20, 2024
  • 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 Seurat.

    epigen/dea_seurat’s past year of commit activity
    R 17 MIT 11 3 0 Updated Dec 20, 2024
  • atacseq_pipeline Public

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

    epigen/atacseq_pipeline’s past year of commit activity
    Python 50 MIT 2 4 0 Updated Dec 20, 2024
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