Projects in Awesome Lists tagged with epigenetics

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/r3fang/SnapATAC

Analysis Pipeline for Single Cell ATAC-seq

bioinformatics-pipeline epigenetics machine-learning-algorithms sequencing single-cell-analysis single-cell-atac-seq

Last synced: 10 May 2025

https://github.com/nanoporetech/tombo

Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.

epigenetics

Last synced: 05 Apr 2025

https://github.com/nanoporetech/megalodon

Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.

basecalling epigenetics guppy variant-calling

Last synced: 29 Mar 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/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/epigen/mrbiomics

MrBiomics: Modules & Recipes augment Bioinformatics for Multi-Omics Analyses

automation bioinformatics biomedical data-science epigenetics framework genetics genomics modules next-generation-sequencing python r recipes research science snakemake workflows

Last synced: 23 Jun 2025

https://github.com/pinellolab/haystack_bio

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

cell chip-seq encode epigenetics epigenomics fimo gene gene-expression haystack-bio haystack-pipeline hotspot motif motifs plasticity regulation rna-seq roadmap specific-regions tfs transcription-factor-binding

Last synced: 06 Feb 2026

https://github.com/kundajelab/chromdragonn

Code for the paper "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts"

chromatin-accessibiity deep-learning epigenetics gene-regulation genomics

Last synced: 27 Jan 2026

https://github.com/aryeelab/hichipper

A preprocessing and QC pipeline for HiChIP data

bioinformatics chromatin-interaction epigenetics hichip

Last synced: 11 Mar 2026

https://github.com/caleblareau/bap

Bead-based single-cell atac processing

bead-doublets epigenetics epigenomics genomics scatac single-cell

Last synced: 10 May 2025

https://github.com/neurogenomics/epicompare

Comparison, benchmarking & QC of epigenetic datasets

benchmark benchmarking bioconductor bioconductor-package comparison epigenetics genetics html interactive-reporting r-package

Last synced: 16 Jan 2026

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/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/qgenlab/diffmethyltools

An automated, end-to-end Python pipeline for differential DNA methylation analysis, region annotation, and visualization.

bioinformatics data-visualization dna-methylation epigenetics python3

Last synced: 11 May 2026

https://github.com/y9c/m6a-camseq

🧪 m6A-CAM-seq

bioinformatics epigenetics rna

Last synced: 06 May 2025

https://github.com/supermaxiste/arpeggio

A SnakeMake workflow to analyse whole genome bisulfite sequencing data from allopolyploids.

allopolyploid automation bisulfite-sequencing dna-methylation epigenetics plants reproducibility snakemake whole-genome-sequencing workflow

Last synced: 04 Mar 2026

https://github.com/kandarprj/epidecoder

Online version of tool is live

differential-expression epigenetics epitranscriptomics genomics genomics-visualization

Last synced: 31 Oct 2025

https://github.com/wvictor14/planet

For inferring ancestry, gestational age, cell type proportions, and preeclampsia status from placental DNA methylation array data

ancestry dna-methylation-data epigenetics genetics inference machine-learning placenta

Last synced: 21 Feb 2026

https://github.com/gabrielhoffman/decorate

Differential Epigenetic Correlation Test

bioconductor correlation epigenetics epigenomics genomics ggplot2 r statistics vizualisation

Last synced: 25 Feb 2026

https://github.com/rushiljalal/quitwise

An android app made using React Native for Appathon 2024

epigenetics expo react-native typescript

Last synced: 05 May 2026

https://github.com/j-andrews7/eclipse

An R package for classifying, comparing, and investigating sub-region structural changes of (super) enhancers (or other large domains).

bioconductor chip-seq classification cutandrun epigenetics regulation super-enhancers

Last synced: 20 Sep 2025

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://github.com/deib-geco/combsafe

Combinatorial and Semantic Analysis of Functional Elements

big-data-analysis chromatin-state epigenetics semantic-annotation

Last synced: 18 Mar 2025

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