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

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

The DKFZ alignment workflow plugin originally developed at the eilslabs

Pipeline for BS-Seq data based on snakemake

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

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

Whole Genome Bisulfite Sequencing Alignment pipeline

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

Our typical analysis steps for WGBS data, starting from FASTQ reads and ending with the construction of bsseq objects. Created using nextflow