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.
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.
genometric.mspc.core
Using combined evidence from replicates to evaluate ChIP-seq peaks
differentialabundance
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
geneXtendeR
R/Bioconductor package for optimized functional annotation of ChIP-seq data
https://github.com/boyle-lab/f-seq2
Improving the feature density based peak caller with dynamic statistics
sevenC
7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
target
target: An R Package to Predict Combined Function of Transcription Factors
manorm2-utils
To pre-process a set of ChIP-seq samples and coordinate with MAnorm2 for differential analysis
https://github.com/kundajelab/chipseq_pipeline
AQUAS TF and histone ChIP-seq pipeline
motifpeeker
Benchmark Epigenomic Profiling Methods with Motif Enrichment as Key Metric
rseb
An R-package for daily tasks required to handle biological data as well as avoid re-coding of small functions for quick but necessary data management.
spikeflow
Pipeline to analyse ChIP-Rx data, i.e ChIP-Seq with reference exogenous genome spike-in normalization
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.
