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300bcg_analysis

300bcg_atacseq_pipeline

artemether_scrna

Single cell RNA-seq analysis of pancreatic islets with drug treatment

atacseq_pipeline

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.

baf_complex

Schick et al 2018 - Systematic functional characterization of BAF mutations yields novel intra-complex synthetic lethalities

base-editor-design-tool

This tool designs guides for use with the base editor technology.

biseqmethcalling

Methylation calling script for bisulfite sequencing

cemm.slurm.sm

CeMM's Snakemake SLURM cluster profile

chipmentation

Data analysis scripts for Schmidl et. al, 2015 (doi:10.1038/nmeth.3542)

cll-chromatin

Data analysis scripts for Rendeiro et. al, 2016 (doi:10.1038/ncomms11938)

cll-ibrutinib

Combined chemosensitivity and chromatin profiling prioritizes drug combinations in CLL

cll-ibrutinib_time

crop-seq

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

dea_limma

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

dea_seurat

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

dnameth500species

Comparative analysis of DNA methylation across more than 500 animal species

enrichment_analysis

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

gbmatch

Code and metadata for glioblastoma matched analysis

genome_tracks

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.

kpnn

Knowledge-primed neural networks

lch_hierarchy

Code for Epigenomics and Single-cell Sequencing Define a Developmental Hierarchy in Langerhans Cell Histiocytosis (Halbritter, Farlik, et al. 2019 Cancer Discov.)

liquorice

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

methylation-biomarker-benchmark

Supplementary code repository accompanying the BLUEPRINT benchmark study of locus-specific DNA methylation assays.

microtest

Small test data from various data types for testing pipelines

mixscape_seurat

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.

mr.pareto

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

mthfd1

open_pipelines

Pipelines for NGS data preprocessing by the Bock lab and friends

picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

rnbeads

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