Projects in Awesome Lists tagged with methylation

https://github.com/jts/nanopolish

Signal-level algorithms for MinION data

bioinformatics c-plus-plus epigenetics genome-assembly methylation science

Last synced: 23 Jan 2026

https://github.com/FelixKrueger/Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

bioinformatics dna methylation

Last synced: 30 Mar 2025

https://github.com/al2na/methylkit

R package for DNA methylation analysis

genome-biology methylation statistical-analysis visualization

Last synced: 20 Oct 2025

https://github.com/nanoporetech/modkit

A bioinformatics tool for working with modified bases

methylation modified-bases nanopore

Last synced: 05 Apr 2025

https://github.com/nanoporetech/remora

Methylation/modified base calling separated from basecalling.

basecalling methylation nanopore

Last synced: 06 Apr 2025

https://github.com/cangermueller/deepcpg

Deep neural networks for predicting CpG methylation

deep-neural-networks deeplearning epigenetics methylation single-cell

Last synced: 14 Jan 2026

https://github.com/bioinfomaticscsu/deepsignal

Detecting methylation using signal-level features from Nanopore sequencing reads

bioinformatics epigenetics methylation nanopore-sequencing tensorflow

Last synced: 01 Jul 2025

https://github.com/bioinfomaticsCSU/deepsignal

Detecting methylation using signal-level features from Nanopore sequencing reads

bioinformatics epigenetics methylation nanopore-sequencing tensorflow

Last synced: 06 May 2025

https://github.com/mehelmy/princess

long-reads methylation phasing single-nucleotide-variation structural-variation

Last synced: 16 Jul 2025

https://github.com/pengni/deepsignal-plant

Detecting methylation using signal-level features from Nanopore sequencing reads of plants

bioinformatics methylation nanopore-sequencing plant pytorch

Last synced: 01 Jul 2025

https://github.com/kdkorthauer/dmrseq

R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing

bioconductor bisulfite-sequencing dmr epigenetics inference methylation

Last synced: 21 Feb 2026

https://github.com/treangenlab/methphaser

MethPhaser: methylation-based haplotype phasing of human genomes

bioinformatics-tool haplotype-blocks methylation

Last synced: 28 Jan 2026

https://github.com/wglab/deepmod2

DNA 5mC methylation detection from Dorado or Guppy basecalled Oxford Nanopore reads

deep-learning methylation nanopore-sequencing

Last synced: 17 Jan 2026

https://github.com/jetbrains-research/bioinf-commons

Bioinformatics library in Kotlin

2bit bam bed bioinformatics cancellable chip-seq dataframe dataset dna-sequence fasta fastq hmm hypothesis-testing kotlin methylation mixture progress sampling

Last synced: 19 Oct 2025

https://github.com/lhqing/cemba_data

Mapping pipeline for snmC-seq based technologies.

methylation pipeline sequencing single-cell snmc-seq snmc-seq2 snmct-seq

Last synced: 01 Apr 2026

https://github.com/andreaskapou/Melissa

Bayesian Clustering and Imputation of Single Cell Methylomes

bayesian-inference clustering imputation methylation variational-inference

Last synced: 09 Apr 2025

https://github.com/reese3928/methylgsa

A Bioconductor package and shiny app for DNA methylation data length bias adjustment in gene set testing

enrichment generalized-linear-models logistic-regression methylation ontology shiny

Last synced: 21 Feb 2026

https://github.com/lkremer/scbs

Python package with CLI for the analysis of single cell methylation data. Now known as MethSCAn: https://github.com/anders-biostat/MethSCAn

dna-methylation dna-methylation-data methylation single-cell single-cell-methylation single-cell-rna-seq

Last synced: 23 Oct 2025

https://github.com/brj0/mepylome

Python toolkit for parsing, processing, and analysis of Illumina methylation array IDAT files

cnv conumee epigenetics illumina methylation methylation-analysis methylation-extractor methylation-microarrays methylation-plot minfi python tumor-classification umap

Last synced: 05 Oct 2025

https://github.com/semenko/serpent-methylation-pipeline

An efficient, documented, reproducible Snakemake methylation analysis pipeline for BS-seq and EM-seq samples, including cfDNA.

bisulfite bs-seq bsseq em-seq emseq epigenetics methylation pipeline snakemake

Last synced: 26 Jan 2026

https://github.com/sing-group/bicycle

bicycle (bisulfite-based methylcytosine caller) is a next-generation sequencing bioinformatics pipeline able to perform a full DNA methylation level analysis

bisulfite bisulfite-sequencing cli dna-methylation java java-bioinformatics methylation

Last synced: 03 Jul 2025

https://github.com/karrlab/bpforms

Toolkit for concretely describing non-canonical DNA, RNA, and proteins

crosslinks dna dna-damage epigenetics methylation phosphorylation post-transcriptional-regulation post-translational-modification protein proteoform rna

Last synced: 25 Jun 2025

https://github.com/dohlee/snakemake-bismark-methyldackel

Bismark-MethylDackel DNA methylation quantification pipeline in snakemake.

bioinformatics methylation pipeline reproducible-research reproducible-science snakemake snakemake-pipelines

Last synced: 05 May 2025

https://github.com/uds-helms/beclear

Correction of batch effects in DNA methylation data

batch-effects bioconductor-package dna-methylation latent-factor-model methylation missing-data missing-values rpackage stochastic-gradient-descent

Last synced: 20 Feb 2026

https://github.com/andrewdavidsmith/transferase

The transferase system for retrieving methylome data from methbase

bisulfite bisulfite-sequencing dna-methylation epigenetics epigenomics methyl-seq methylation methylation-analysis methylome wgbs

Last synced: 10 Oct 2025

https://xwanglabthu.github.io/ARIC/

Accurate and robust inference of cell type proportions from bulk gene expression or DNA methylation data

deconvolution methylation rna-seq

Last synced: 20 Apr 2025

https://github.com/yoannpa/computational_epigenomics

This repository contains data and functions related to computational epigenomics data analysis.

450k beta-values bioinformatics computational-epigenomics coverage dataprocessing epigenomics human-methylation-450k methylation wgbs

Last synced: 23 Feb 2026

https://github.com/mcwdsi/bam2tensor

Convert methylation data to sparse objects for machine learning.

machine-learning methylation

Last synced: 12 May 2026

https://github.com/jcaperella29/methylation_shiny

An interactive R Shiny web app for DNA methylation analysis with support for DE, pathway enrichment, power analysis, and machine learning — deployable on HPC via Singularity/Apptainer.

apptainer bioconductor bioinformatics data-visualization differential-expression epigenetics genomics machine-learning methylation pathway-enrichment-analysis pca r random-forest shiny singularity umap

Last synced: 02 Aug 2025

https://github.com/vsubasri/lfs-germline

Multiple germline events lead to cancer development in patients with Li-Fraumeni syndrome

cancer-genomics epimutation germline-variants hereditary-cancer-syndrome methylation

Last synced: 10 Jul 2026

https://github.com/mullinslab/methylation-station

An application for analyzing and visualizing DNA methylation in multiple sequence alignments

bioinformatics methylation sequence-analysis visualization

Last synced: 03 Jul 2026

https://github.com/dohlee/snakemake-bismark-methyldackel-sra

Process SRA bisulfite sequencing data easily with Bismark-MethylDackel pipeline.

bioinformatics bismark methylation pipeline snakemake

Last synced: 15 May 2026

https://github.com/wvictor14/plomics

Personal library for analyzing genomic data...

27 450k analysis array dna dnam epic methylation

Last synced: 16 Jul 2026

https://github.com/harshavardhan9241/multi-omics-diablo-pipeline

This repository offers R scripts for integrating transcriptomics, methylation, and proteomics data using the DIABLO method. Explore the code to streamline your multi-omics analysis and enhance your research insights! 🐙📊

450k betavalue bioconductor biomarkers diablo illumina integrative-analysis methylation multiomics r rppa