wgbs

Analysis pipelines for genomic sequencing data

Multi-omics analysis protocols by Lyu.

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)

Differential methylation: Easy, Fast, Identification and ANnoTation

AnaLysis routines for ePigenomicS data - 🏫 Bioconductor project

Methylation analysis pipeline for genome graph

TFregulomeR reveals transcription factors’ context-specific features and functions

Cluster-based analysis of CpG methylation

R package to impute methylation within WGBS using machine learning

An R package for weighted region comethylation network analysis

A pipeline to identify differentially-methylated regions from whole-genome bisulfite sequencing data

Pipeline for BS-Seq data based on snakemake

The DKFZ alignment workflow plugin originally developed at the eilslabs

The transferase system for retrieving methylome data from methbase

Genomic Annotation Visualization R package.

Analysis scripts for identification and visualization of Wilson disease-associated DNA methylation changes in human liver and blood

Snakemake Workflow For Running Biscuit https://github.com/huishenlab/biscuit