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

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

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.

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.

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.

CeMM's Snakemake SLURM cluster profile

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

Knowledge-primed neural networks

Pipelines for NGS data preprocessing by the Bock lab and friends