There are 2 repositories under wgbs topic.
A R package and executable for the preprocessing, statistical analysis, and downstream testing and visualization of differentially methylated regions (DMRs) from CpG count matrices (Bismark cytosine reports)
A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.
ENCODE whole-genome bisulfite sequencing (WGBS) pipeline
A whole genome bisulfite sequencing (WGBS) pipeline for the alignment and QC of DNA methylation that goes from from raw reads (FastQ) to a CpG count matrix (Bismark cytosine reports)
TFregulomeR reveals transcription factors’ context-specific features and functions
An R package for weighted region comethylation network analysis
The DKFZ alignment workflow plugin originally developed at the eilslabs
A pipeline to identify differentially-methylated regions from whole-genome bisulfite sequencing data
Pipeline for BS-Seq data based on snakemake
Analysis scripts for identification and visualization of Wilson disease-associated DNA methylation changes in human liver and blood
An example script of how to download WGBS data from SLIMS, check md5sums, merge lanes, and submit a project to CpG_Me
TFregulomeR reveals transcription factors’ context-specific features and functions
Analyses for the manuscript "Prenatal PCB exposure alters a shared neurodevelopmental DNA methylation profile in mouse placenta and fetal brain".
Snakemake Workflow For Running Biscuit https://github.com/huishenlab/biscuit
Our typical analysis steps for WGBS data, starting from FASTQ reads and ending with the construction of bsseq objects. Created using nextflow
A Bioconductor ExperimentHub data package for flow sorted purified whole blood cell types measured using DNA methylation on WGBS platform from BLUEPRINT
This repository contains data and functions related to computational epigenomics data analysis.
Analysis of DNA methylation data by whole-genome bisulfite sequencing in umbilical cord blood from ASD and TD subjects in the MARBLES and EARLI studies
Analysis of DNA methylation and gene expression for thioredoxin system genes in Wilson disease
mix of python, bash and R functions, scripts and notebooks to benchmark the use of methylation as proxy to infer TF binding
Using Snakemake to implement ENCODE WGBS pipeline