Discover epigen/methylation-biomarker-benchmark Open Source project

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R
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MIT License
Created almost 9 years ago
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Supplementary code repository accompanying the BLUEPRINT benchmark study of locus-specific DNA methylation assays.

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.

Python

KPNN

Knowledge-primed neural networks

Python

crop-seq

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

Python

enrichment_analysis

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

Python

open_pipelines

Pipelines for NGS data preprocessing by the Bock lab and friends

Python

unsupervised_analysis

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

Python

mr.pareto

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

Python

dea_limma

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

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.

Python

scrnaseq_processing_seurat

A Snakemake workflow 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.

scifiRNA-seq

Python

dea_seurat

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

spilterlize_integrate

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.

Python

scifiRNA-seq_publication

The million-scale method for single-cell analysis

Jupyter Notebook

cemm.slurm.sm

CeMM's Snakemake SLURM cluster profile

Shell

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.

LIQUORICE

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

Python

cll-chromatin

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

Python

GBMatch

Code and metadata for glioblastoma matched analysis

chipmentation

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

Python

DNAmeth500species

Comparative analysis of DNA methylation across more than 500 animal species

Jupyter Notebook

Artemether_scRNA

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

baf_complex

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

Jupyter Notebook

cll-ibrutinib_time

RnBeads_web

RnBeads website and online resources

HTML

microtest

Small test data from various data types for testing pipelines

Shell

300BCG_analysis

Jupyter Notebook

epigen/methylation-biomarker-benchmark

epigen

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