Projects in Awesome Lists by epigen

https://github.com/epigen/atacseq_pipeline

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

atac-seq bash bioinformatics biomedical-data-science ngs pipeline python snakemake workflow

Last synced: 07 Mar 2026

https://github.com/epigen/cellwhisperer

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

Last synced: 15 Apr 2025

https://github.com/epigen/mrbiomics

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

automation bioinformatics biomedical data-science epigenetics framework genetics genomics modules next-generation-sequencing python r recipes research science snakemake workflows

Last synced: 23 Jun 2025

https://github.com/epigen/enrichment_analysis

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

atac-seq bioinformatics biomedical-data-science chip-seq enrichment-analysis gene-set-enrichment gene-sets genomic-regions motif-enrichment-analysis pipeline rna-seq snakemake visualization workflow

Last synced: 15 Apr 2025

https://github.com/epigen/kpnn

Knowledge-primed neural networks

Last synced: 26 Feb 2026

https://github.com/epigen/dea_limma

A Snakemake workflow and MrBiomics module for performing and visualizing differential (expression) analyses (DEA) on NGS data powered by the R package limma.

atac-seq bioinformatics biomedical-data-science chip-seq differential-expression-analysis limma limma-trend limma-voom r rna-seq scrna-seq snakemake statistics visualization volcano-plot workflow

Last synced: 15 Apr 2025

https://github.com/epigen/unsupervised_analysis

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

cluster-analysis cluster-validation clustering clustering-algorithm clustree data-science data-visualization densmap dimensionality-reduction heatmap high-dimensional-data leiden-algorithm pca principal-component-analysis snakemake umap unsupervised-learning visualization workflow

Last synced: 15 Apr 2025

https://github.com/epigen/genome_tracks

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.

atac-seq bioinformatics biomedical-data-science genome-browser genome-track genomic-regions pipeline python rna-seq scrna-seq snakemake visualization workflow

Last synced: 15 Apr 2025

https://github.com/epigen/scrnaseq_processing_seurat

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.

10xgenomics bioinformatics biomedical-data-science cite-seq sccrispr-seq scrna-seq single-cell snakemake snrna-seq visualization workflow

Last synced: 15 Apr 2025

https://github.com/epigen/open_pipelines

Pipelines for NGS data preprocessing by the Bock lab and friends

atac-seq bioinformatics chip-seq looper ngs-pipeline pipeline pypiper rna-seq

Last synced: 11 Aug 2025

https://github.com/epigen/dea_seurat

A Snakemake workflow and MrBiomics module for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R package Seurat.

bioinformatics biomedical-data-science differential-expression-analysis scrna-seq single-cell snakemake snrna-seq visualization volcano-plot workflow

Last synced: 14 Jun 2025

https://github.com/epigen/mixscape_seurat

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.

bioinformatics biomedical-data-science perturbation-analysis sccrispr-seq scrna-seq single-cell snakemake snrna-seq visualization workflow

Last synced: 22 Aug 2025

https://github.com/epigen/spilterlize_integrate

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.

atac-seq batch-effect bioinformatics biomedical-data-science chip-seq confounding-effects count-matrix dimensionality-reduction integration ngs normalization pipeline rna-seq snakemake visualization workflow