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@epigen

Computational Epigenetics

Computational Epigenetics Research and Software

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  1. microtest microtest Public

    Small test data from various data types for testing pipelines

    Shell 1 3

  2. open_pipelines open_pipelines Public

    Pipelines for NGS data preprocessing by the Bock lab and friends

    Python 20 11

Repositories

Showing 10 of 37 repositories
  • genome_tracks Public

    A Snakemake workflow for easy visualization of genome browser tracks of aligned BAM files (e.g., RNA-seq, ATAC-seq, scRNA-seq, ...) powered by the wrapper gtracks for the package pyGenomeTracks, and IGV-reports.

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

    A Snakemake workflow to split, filter, normalize, integrate and select highly variable features of count matrices resulting from experiments with sequencing readout (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including diagnostic visualizations.

    epigen/spilterlize_integrate’s past year of commit activity
    Python 10 MIT 0 3 0 Updated Aug 29, 2024
  • unsupervised_analysis Public

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

    epigen/unsupervised_analysis’s past year of commit activity
    Python 20 MIT 3 20 0 Updated Aug 22, 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 17 MIT 0 4 0 Updated Aug 22, 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 15 MIT 1 11 0 Updated Aug 13, 2024
  • 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 13 23 0 Updated Jul 18, 2024
  • enrichment_analysis Public

    A Snakemake workflow 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 22 MIT 1 0 0 Updated Jul 7, 2024
  • dea_seurat Public

    A Snakemake workflow 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 11 MIT 10 2 0 Updated May 27, 2024
  • RnBeads_web Public

    RnBeads website and online resources

    epigen/RnBeads_web’s past year of commit activity
    HTML 1 MIT 0 0 0 Updated May 15, 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 42 MIT 2 4 0 Updated May 8, 2024
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