dna-methylation
There are 5 repositories under dna-methylation topic.
nf-core / methylseq
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
Language:Nextflow 131- Language:Python 130
nloyfer / wgbs_tools
tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
Language:Python 119xie186 / ViewBS
ViewBS - a powerful toolkit for visualization of high-throughput bisulfite sequencing data
Language:Perl 81crazyhottommy / DNA-methylation-analysis
DNA methylation analysis notes from Ming Tang
- Language:C 63
- Language:R 48
- metheor
dohlee / metheor
:comet: Ultrafast DNA methylation heterogeneity calculation from bisulfite alignments (Lee et al., PLOS Computational Biology. 2023)
Language:Rust 41 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)
Language:R 38- Language:Python 33
jlab-code / MethylStar
A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.
Language:Python 30- methrix
CompEpigen / methrix
An R :package: for fast and flexible DNA methylation analysis
Language:R 27 - nanome
LabShengLi / nanome
NANOME pipeline (Nanopore long-read sequencing data consensus DNA methylation detection)
Language:Python 27 - Language:Python 27
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)
Language:Shell 20andreaskapou / BPRMeth
Modelling DNA methylation profiles
Language:R 19- Language:R 17
benoukraflab / TFregulomeR-old
TFregulomeR reveals transcription factors’ context-specific features and functions
Language:R 16qzhang314 / DNAm-based-age-predictor
A chronological age predictor based on DNA methylation
Language:R 16transbioZI / BioMM
BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data
Language:HTML 14MicrobialDarkMatter / nanomotif
Nanomotif - a tool for identifying methylated motifs in metagenomic samples
Language:Python 12- deconvR
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.
Language:R 10 - Language:R 10
- Language:R 10
jordiabante / CpelAsm.jl
Julia module to perform haplotype allele-specific DNA methylation analysis.
Language:Julia 10- Language:Python 10
aldringsvitenskap / epigeneticclock
Calculate DNA methylation age using Horvath 2013 method
Language:R 9LieberInstitute / Alzheimers_DNAm
Epigenome-wide analysis of DNA methylation from Alzheimer's patients and unaffected controls
Language:R 9hellosunking / Msuite2
Msuite2: integrated DNA methylation data analysis toolkit with enhanced performance
Language:C++ 8- methylrLanguage:HTML 8
- Language:Python 8
sing-group / bicycle
bicycle (bisulfite-based methylcytosine caller) is a next-generation sequencing bioinformatics pipeline able to perform a full DNA methylation level analysis
Language:Java 8cemordaunt / comethyl
An R package for weighted region comethylation network analysis
Language:R 7mwsill / mnp_training
DNA methylation-based classification of central nervous system tumours
Language:HTML 7A pipeline to identify differentially-methylated regions from whole-genome bisulfite sequencing data
Language:R 6seb-mueller / snakemake-bisulfite
Pipeline for BS-Seq data based on snakemake
Language:Python 6
