epigen repositories

unsupervised_analysis

Public

A general purpose Snakemake workflow and MrBiomics module to perform unsupervised analyses (dimensionality reduction & cluster analysis) and visualizations of h…

visualization workflow data-science

visualization workflow data-science snakemake clustering heatmap data-visualization high-dimensional-data pca dimensionality-reduction

Python

•

MIT License

•4•67•20•0•Updated

Apr 21, 2026

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 RcisTarg…

visualization workflow bioinformatics

visualization workflow bioinformatics gene-sets rna-seq snakemake pipeline chip-seq atac-seq gene-set-enrichment

Python

•

MIT License

•4•76•2•0•Updated

Apr 16, 2026

IgManalyser

Public

Code for the IgM array preprocessing and downstream analysis

R

•

MIT License

•0•0•0•0•Updated

Apr 8, 2026

MrBiomics

Public

MrBiomics: Composable modules and recipes automate bioinformatics for multi-omics analyses

python science recipes

python science recipes data-science automation bioinformatics snakemake framework r research

R

•

MIT License

•3•168•31•0•Updated

Apr 1, 2026

dea_limma

Public

A Snakemake workflow and MrBiomics module for performing and visualizing differential analyses of NGS data powered by the R package limma.

visualization workflow bioinformatics

visualization workflow bioinformatics rna-seq snakemake r statistics dea scrna-seq chip-seq

R

•

MIT License

•2•64•0•0•Updated

Mar 24, 2026

RnBeads

Public

Git working Repo synced to the Bioconductor: http://bioconductor.org/packages/devel/bioc/html/RnBeads.html

R

•14•8•26•1•Updated

Mar 16, 2026

CellWhisperer

Public

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

Jupyter Notebook

•

GNU General Public License v3.0

•27•201•3•0•Updated

Mar 9, 2026

cellxgene

Public

Fork of `cellxgene` repository with adaptations for CellWhisperer and SpotWhisperer

JavaScript

•

MIT License

•1•0•1•1•Updated

Mar 5, 2026

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 fi…

visualization workflow bioinformatics

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

R

•

MIT License

•3•59•4•0•Updated

Jan 29, 2026

spilterlize_integrate

Public

A Snakemake workflow and MrBiomics module to split, filter, normalize, integrate and select highly variable features of count matrices resulting from next-gener…

visualization workflow bioinformatics

visualization workflow bioinformatics rna-seq snakemake integration pipeline ngs dimensionality-reduction chip-seq

R

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MIT License

•3•54•1•0•Updated

Jan 9, 2026

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) p…

visualization workflow bioinformatics

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

R

•

MIT License

•2•56•2•0•Updated

Dec 7, 2025

atacseq_pipeline

Public

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

python bash workflow

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

Python

•

MIT License

•2•101•3•0•Updated

Nov 25, 2025

cemm.slurm.sm

Public

CeMM's Snakemake SLURM cluster profile

snakemake slurm cluster-profile

Python

•

MIT License

•2•50•0•0•Updated

Oct 8, 2025

UCE

Public

UCE is a zero-shot foundation model for single-cell gene expression data

Python

•

MIT License

•35•0•0•0•Updated

Sep 29, 2025

LLaVA

Public

This is a fork of the llava project with adaptations for CellWhisperer

Python

•

Apache License 2.0

•0•0•0•0•Updated

Sep 24, 2025

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 Seura…

visualization workflow bioinformatics

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

R

•

MIT License

•11•56•3•0•Updated

Sep 5, 2025

ShinyCell2

Public

Fork of ShinyCell2 customised for SD/LDR HEACA Atlas.

R

•

GNU General Public License v3.0

•13•0•0•0•Updated

Aug 27, 2025

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…

visualization python workflow

visualization python workflow bioinformatics rna-seq snakemake pipeline scrna-seq atac-seq genome-browser

Python

•

MIT License

•1•57•2•0•Updated

Aug 5, 2025

rnaseq_pipeline

Public

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

python bash workflow

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

Python

•

MIT License

•2•45•1•0•Updated

Aug 5, 2025

macrophage-regulation

Public

Integrated time-series analysis and high-content CRISPR screening delineate the dynamics of macrophage immune regulation

bioinformatics rna-seq time-series

bioinformatics rna-seq time-series systems-biology scrna-seq crispr immunology atac-seq transcriptomics epigenomics

Jupyter Notebook

•

MIT License

•0•5•0•0•Updated

Jul 20, 2025

fetch_ngs

Public

Workflow to Fetch Public Sequencing Data and Metadata Using iSeq and MrBiomics Module.

database repository genomics

database repository genomics ngs next-generation-sequencing bam fastq

Python

•

MIT License

•0•45•1•0•Updated

Jun 23, 2025

RnBeads_web

Public

RnBeads website and online resources

HTML

•

MIT License

•1•1•0•0•Updated

Apr 10, 2025

scEval

Public

Bock lab fork of scEval

Jupyter Notebook

•11•0•0•0•Updated

Dec 28, 2024

Geneformer

Public

Private fork of Geneformer

Python

•0•1•0•0•Updated

Oct 3, 2024

300BCG_analysis

Public

Jupyter Notebook

•1•3•1•0•Updated

Jan 8, 2024

300BCG_ATACseq_pipeline

Public

Jupyter Notebook

•0•0•0•0•Updated

Jan 8, 2024

scifiRNA-seq_publication

Public

The million-scale method for single-cell analysis

Jupyter Notebook

•0•10•2•4•Updated

Jul 6, 2023

LIQUORICE

Public

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

Python

•

GNU General Public License v3.0

•6•10•0•0•Updated

Mar 30, 2023

KPNN

Public

Knowledge-primed neural networks

Python

•

GNU General Public License v3.0

•8•38•0•2•Updated

Mar 24, 2023

DNAmeth500species

Public

Comparative analysis of DNA methylation across more than 500 animal species

Jupyter Notebook

•4•6•1•0•Updated

Oct 11, 2022

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Bock Lab @ CeMM & Medical University of Vienna

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48 repositories

unsupervised_analysis

enrichment_analysis

IgManalyser

MrBiomics

dea_limma

RnBeads

CellWhisperer

cellxgene

scrnaseq_processing_seurat

spilterlize_integrate

mixscape_seurat

atacseq_pipeline

cemm.slurm.sm

UCE

LLaVA

dea_seurat

ShinyCell2

genome_tracks

rnaseq_pipeline

macrophage-regulation

fetch_ngs

RnBeads_web

scEval

Geneformer

300BCG_analysis

300BCG_ATACseq_pipeline

scifiRNA-seq_publication

LIQUORICE

KPNN

DNAmeth500species

All

All

Repositories list

48 repositories