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@epigen

Computational Epigenetics

Computational Epigenetics Research and Software

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  1. CellWhisperer Public

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

    Jupyter Notebook 51 7

  2. MrBiomics Public

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

    Python 45 1

  3. atacseq_pipeline Public

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

    Python 51 2

  4. KPNN Public

    Knowledge-primed neural networks

    Python 35 8

  5. 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 Public archive

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

    Python 30 13

Repositories

Showing 10 of 44 repositories
  • 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.

    R 24 MIT 2 4 0 Updated Mar 6, 2025
  • 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 24 MIT 4 23 0 Updated Mar 4, 2025
  • 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.

    R 14 MIT 3 0 0 Updated Mar 4, 2025
  • UCE Public Forked from snap-stanford/UCE

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

    Python 0 MIT 34 0 0 Updated Feb 13, 2025
  • RnBeads Public Forked from cirruswolke/RnBeads

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

    R 7 12 23 0 Updated Feb 6, 2025
  • 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 MIT 2 3 0 Updated Jan 31, 2025
  • cellxgene Public

    Bare clone of cellxgene

    JavaScript 0 MIT 0 0 1 Updated Jan 27, 2025
  • scEval Public Forked from HelloWorldLTY/scEval

    Bock lab fork of scEval

    Jupyter Notebook 0 10 0 0 Updated Dec 28, 2024
  • MrBiomics Public

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

    Python 45 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.

    R 16 MIT 2 1 0 Updated Dec 20, 2024
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