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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 33 5

  2. mr.pareto mr.pareto Public

    MR.PARETO - Modules & Recipes for Pragmatic Augmentation of Research Efficiency Towards Optimum

    Python 23 1

  3. atacseq_pipeline atacseq_pipeline Public

    Ultimate ATAC-seq Data Processing & Quantification Workflow. A Snakemake implementation of the BSF's ATAC-seq Data Processing Pipeline extended by downstream quantification and annotation steps usi…

    Python 43 2

  4. KPNN KPNN Public

    Knowledge-primed neural networks

    Python 34 8

  5. crop-seq crop-seq Public archive

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

    Python 29 12

  6. enrichment_analysis enrichment_analysis Public

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

    Python 26 1

Repositories

Showing 10 of 42 repositories
  • cellxgene Public

    Bare clone of cellxgene

    epigen/cellxgene’s past year of commit activity
    JavaScript 0 MIT 0 0 1 Updated Oct 28, 2024
  • 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 33 GPL-3.0 5 2 0 Updated Oct 18, 2024
  • dea_limma Public

    A Snakemake workflow 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 18 MIT 1 9 1 Updated Oct 18, 2024
  • Geneformer Public

    Private fork of Geneformer

    epigen/Geneformer’s past year of commit activity
    Python 1 0 0 0 Updated Oct 3, 2024
  • scrnaseq_processing_seurat Public

    A Snakemake workflow 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 11 MIT 1 6 0 Updated Oct 2, 2024
  • LLaVA Public
    epigen/LLaVA’s past year of commit activity
    Python 0 Apache-2.0 0 0 0 Updated Oct 1, 2024
  • mr.pareto Public

    MR.PARETO - Modules & Recipes for Pragmatic Augmentation of Research Efficiency Towards Optimum

    epigen/mr.pareto’s past year of commit activity
    Python 23 MIT 1 16 0 Updated Sep 25, 2024
  • atacseq_pipeline Public

    Ultimate ATAC-seq Data Processing & Quantification Workflow. A Snakemake implementation of the BSF's ATAC-seq Data Processing Pipeline extended by downstream quantification and annotation steps using bash and Python.

    epigen/atacseq_pipeline’s past year of commit activity
    Python 43 MIT 2 4 0 Updated Sep 18, 2024
  • rnaseq_pipeline Public Forked from snakemake-workflows/rna-seq-star-deseq2

    RNA-seq Data Processing, Quantification and Annotation Workflow.

    epigen/rnaseq_pipeline’s past year of commit activity
    Python 1 MIT 203 1 0 Updated Sep 15, 2024
  • mixscape_seurat Public

    A Snakemake workflow 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 10 MIT 1 1 0 Updated Sep 13, 2024
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