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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 45 7

  2. MrBiomics MrBiomics Public

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

    Python 41 1

  3. atacseq_pipeline atacseq_pipeline Public

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

    Python 48 2

  4. KPNN KPNN Public

    Knowledge-primed neural networks

    Python 34 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 42 repositories
  • 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 14 MIT 1 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 16 MIT 11 2 0 Updated Dec 20, 2024
  • 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 6 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 48 MIT 2 4 0 Updated Dec 20, 2024
  • genome_tracks Public

    A Snakemake workflow and MrBiomics module 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 19 MIT 1 2 0 Updated Dec 20, 2024
  • spilterlize_integrate Public

    A Snakemake workflow and MrBiomics module 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 14 MIT 3 6 1 Updated Dec 20, 2024
  • 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.

    epigen/unsupervised_analysis’s past year of commit activity
    Python 26 MIT 4 28 5 Updated Dec 20, 2024
  • 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.

    epigen/enrichment_analysis’s past year of commit activity
    Python 32 MIT 2 2 0 Updated Dec 20, 2024
  • MrBiomics Public

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

    epigen/MrBiomics’s past year of commit activity
    Python 41 MIT 1 20 0 Updated Dec 16, 2024
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