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@epigen

Computational Epigenetics

Computational Epigenetics Research and Software

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  1. mr.pareto mr.pareto Public

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

    Python 19 1

  2. 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 42 2

  3. KPNN KPNN Public

    Knowledge-primed neural networks

    Python 34 8

  4. crop-seq crop-seq Public archive

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

    Python 29 12

  5. open_pipelines open_pipelines Public

    Pipelines for NGS data preprocessing by the Bock lab and friends

    Python 20 11

  6. LIQUORICE LIQUORICE Public

    A tool to detect tissue- and cancer- specific epigenetic signatures in WGS data of liquid biopsies

    Python 9 5

Repositories

Showing 10 of 39 repositories
  • 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 0 Updated Sep 26, 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 19 MIT 1 13 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 42 MIT 2 5 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 198 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
  • 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 Sep 13, 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 0 7 0 Updated Sep 13, 2024
  • 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 2 0 Updated Sep 13, 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 24 MIT 1 1 0 Updated Sep 13, 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 Sep 13, 2024
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