Analysis pipelines for genomic sequencing data

• UpdatedMar 17, 2025
• Shell

Multi-omics analysis protocols by Lyu.

• UpdatedAug 22, 2023
• HTML

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)

• UpdatedOct 10, 2023
• R

A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.

• UpdatedSep 24, 2021
• Python

ENCODE whole-genome bisulfite sequencing (WGBS) pipeline

• UpdatedFeb 15, 2022
• Python

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)

• UpdatedMar 28, 2022
• Shell

Differential methylation: Easy, Fast, Identification and ANnoTation

• UpdatedDec 18, 2020
• Shell

AnaLysis routines for ePigenomicS data - 🏫 Bioconductor project

• UpdatedJul 7, 2023
• R

TFregulomeR reveals transcription factors’ context-specific features and functions

• UpdatedApr 18, 2022
• R

Cluster-based analysis of CpG methylation

• UpdatedJan 11, 2024
• Python

R package to impute methylation within WGBS using machine learning

• UpdatedMar 9, 2023
• R

Methylation analysis pipeline for Genome Graph

• UpdatedMar 4, 2025
• Python

An R package for weighted region comethylation network analysis

• UpdatedOct 14, 2023
• R

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

• UpdatedMay 15, 2020
• R

The DKFZ alignment workflow plugin originally developed at the eilslabs

• UpdatedOct 5, 2023
• Python

Pipeline for BS-Seq data based on snakemake

• UpdatedApr 1, 2022
• Python

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

• UpdatedJun 24, 2019
• R

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

• UpdatedSep 15, 2023
• HTML

Whole Genome Bisulfite Sequencing Alignment pipeline

• UpdatedJul 13, 2017
• Shell

An example script of how to download WGBS data from SLIMS, check md5sums, merge lanes, and submit a project to CpG_Me

• UpdatedFeb 28, 2020
• Shell