A course on genomics and bioinformatics from WU

Project Manager for NGS data analysis

Pipelines in genomics

Pipeline for Analysis of ChIP-Seq data

A pre-cooked version of our course

cisVar scripts.

An R package containing bioinformatics utility functions. Mostly related to RNAseq data analysis

🖥️🧬 Materials for a Bioinformatics Workshop on ChIP-seq analysis, introduction to R and GenomicRanges.

A command-line toolkit for summarizing, analyzing, and interpreting ChIP-Seq and RNA-Seq experiments, designed for enhancer and super-enhancer region analysis in tumor-normal pairs, with applications in differential enrichment and multi-sample domain analysis.

R package for exploratory analysis of ChIPseq data

Pipeline to process RNAseq and ChIPseq data. Outputs include gene counts, transcripts per million, alternate splicing events, SNP calls, and bigwigs. Supports both Docker and Singularity for all dependencies.

util scripts for various omics data analysis

target: An R Package to Predict Combined Function of Transcription Factors (workflow article)

Workflows for correlation of Expression and peaks with file quality, related to our paper "Overlooked poor-quality patient samples in sequencing data impair reproducibility of published clinically relevant datasets"

Which ESR1 and PGR binding sites are functional?

A snakemake based workflow for ChIPSeq data analysis

Genomic regions (e.g ChIPseq peaks) annotation with TxDB object

A technical note to describe the segmenter package