🖥️🧬 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.

cisVar scripts.

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"

A snakemake based workflow for ChIPSeq data analysis

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.

A technical note to describe the segmenter package

Snakemake Pipeline for the Analyses of ChIP-seq data in Cancer samples

Package demo slides, "Chromatin Segmentation Analysis in R"

This is a repository to show my experience analyzing different kinds of Omics data.

dbFinder code

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

Differential peak analysis, genomic sequences associated with distinct experimental conditions

Which ESR1 and PGR binding sites are functional?

R package for exploratory analysis of ChIPseq data

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

Pipelines in genomics