dna-methylation
There are 127 repositories under dna-methylation topic.
nf-core/methylseq
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
nloyfer/wgbs_tools
tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
yupenghe/methylpy
WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
xie186/ViewBS
ViewBS - a powerful toolkit for visualization of high-throughput bisulfite sequencing data
crazyhottommy/DNA-methylation-analysis
DNA methylation analysis notes from Ming Tang
zwdzwd/sesame
🍪 SEnsible Step-wise Analysis of DNA MEthylation BeadChips
zhou-lab/biscuit
BISulfite-seq CUI Toolkit
dohlee/metheor
:comet: Ultrafast DNA methylation heterogeneity calculation from bisulfite alignments (Lee et al., PLOS Computational Biology. 2023)
ben-laufer/DMRichR
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)
lhqing/ALLCools
Toolkit for single-cell DNA methylation analysis.
jlab-code/MethylStar
A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.
CompEpigen/methrix
An R :package: for fast and flexible DNA methylation analysis
LabShengLi/nanome
NANOME pipeline (Nanopore long-read sequencing data consensus DNA methylation detection)
yupenghe/REPTILE
Predicting regulatory DNA elements based on epigenomic signatures
MicrobialDarkMatter/nanomotif
Nanomotif - a tool for identifying methylated motifs in metagenomic samples
ben-laufer/CpG_Me
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)
andreaskapou/BPRMeth
Modelling DNA methylation profiles
qzhang314/DNAm-based-age-predictor
A chronological age predictor based on DNA methylation
sartorlab/methylSig
R package for DNA methylation analysis
benoukraflab/TFregulomeR-old
TFregulomeR reveals transcription factors’ context-specific features and functions
transbioZI/BioMM
BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data
JD2112/methylr
methylR: a single shiny solution from sequencer data to pathway analysis
anders-biostat/MethSCAn
Python package with CLI for the analysis of single cell methylation data.
aldringsvitenskap/epigeneticclock
Calculate DNA methylation age using Horvath 2013 method
BIMSBbioinfo/deconvR
The deconvR is an R package designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model.
cgplab/PAMES
Tool to estimate purity of tumor samples exploiting DNA Methylation data
databio/COCOA
Annotating epigenetic variation among samples with region sets in R
hellosunking/Msuite2
Msuite2: integrated DNA methylation data analysis toolkit with enhanced performance
jordiabante/CpelAsm.jl
Julia module to perform haplotype allele-specific DNA methylation analysis.
LieberInstitute/Alzheimers_DNAm
Epigenome-wide analysis of DNA methylation from Alzheimer's patients and unaffected controls
cemordaunt/comethyl
An R package for weighted region comethylation network analysis
cemordaunt/DMRfinder
A pipeline to identify differentially-methylated regions from whole-genome bisulfite sequencing data
JiejunShi/CAMDA
Quantify the Concurrence of DNA Methylation and De-methylation
sing-group/bicycle
bicycle (bisulfite-based methylcytosine caller) is a next-generation sequencing bioinformatics pipeline able to perform a full DNA methylation level analysis
benoukraflab/TFregulomeR
TFregulomeR reveals transcription factors’ context-specific features and functions
YaoLi3/nanopore-methylation
Long sequencing reads classifier