Projects in Awesome Lists tagged with epigenomics
A curated list of projects in awesome lists tagged with epigenomics .
https://github.com/Novartis/peax
Peax is a tool for interactive visual pattern search and exploration in epigenomic data based on unsupervised representation learning with autoencoders
autoencoder data-visualization deep-learning epigenomics interactive-machine-learning pattern-search sequential-data
Last synced: 07 May 2025
https://github.com/dohlee/metheor
:comet: Ultrafast DNA methylation heterogeneity calculation from bisulfite alignments (Lee et al., PLOS Computational Biology. 2023)
bioinformatics computational-biology computational-epigenomics dna-methylation epigenomics rust
Last synced: 29 Apr 2025
https://github.com/dohlee/chromoformer
The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)
artificial-intelligence bioinformatics deep-learning epigenomics gene-expression genomics histone-modifications transcriptomics transformer
Last synced: 29 Apr 2025
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/lieberinstitute/alzheimers_dnam
Epigenome-wide analysis of DNA methylation from Alzheimer's patients and unaffected controls
450k alzheimers-disease dna-methylation epigenomics
Last synced: 07 May 2025
https://github.com/rnajena/magnipore
Magnipore: Differential single nucleotide changes of ONT signals
comparative-analysis epigenomics epitranscriptomics ont oxford-nanopore raw-signal
Last synced: 27 Nov 2024
https://github.com/epigen/macrophage-regulation
Integrated time series analysis and high-content CRISPR screening delineates the dynamics of macrophage immune regulation
atac-seq bioinformatics crispr crop-seq epigenomics immunology perturb-seq perturbations rna-seq scrna-seq systems-biology systems-immunology time-series transcriptomics
Last synced: 15 May 2025
https://github.com/crazyhottommy/pyflow-chromforest
snakemake workflow for random forest based feature selection on chromHMM data
chromhmm epigenomics machine-learning snakemake-workflows
Last synced: 06 May 2025
https://github.com/neurogenomics/motifpeeker
Benchmark Epigenomic Profiling Methods with Motif Enrichment as Key Metric
bioconductor bioconductor-package chip-seq epigenomics interactive-report motif-enrichment-analysis r-package
Last synced: 03 Apr 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: 06 Apr 2025
https://github.com/neurogenomics/peakyfinders
R package for mining, calling, and importing epigenomic peaks.
encode epigenomics gene-expression-omnibus genomics peak-calling r r-package
Last synced: 03 Apr 2025
https://github.com/neurogenomics/cutntag-benchmarking-analysis
Processing, benchmarking and analysis of CUT&Tag against ENCODE ChIP-seq.
cutandtag-seq epigenomics histone-modifications
Last synced: 03 Apr 2025
https://github.com/neurogenomics/epiprepare
Preprocessing of epigenomic data from fastq files.
epigenomics next-generation-sequencing preprocessing r r-package
Last synced: 03 Apr 2025
https://github.com/matthiaszepper/thesis
My PhD thesis: Epigenetic characterization of murine Dnmt1-deficient MLL-AF9 leukemia
bioinformatics bioinformatics-tool cancer-genomics cancer-research epigenomics genetics
Last synced: 13 Mar 2025
https://github.com/zsteve/nf-atac
ATAC-seq pipeline written in Nextflow
atac-seq bioinformatics epigenomics nextflow ngs pipeline
Last synced: 29 Mar 2025
https://github.com/neurogenomics/epiarchives
Public archive for EpiCompare reports.
database epigenomics r reproducible-research workflows
Last synced: 03 Apr 2025
https://github.com/neurogenomics/motifpeeker-reports
Public archive of reports generated using MotifPeeker R package
database epigenomics r reproducible-research
Last synced: 03 Apr 2025
https://github.com/neurogenomics/cut_n_tag
Preprocessing pipeline for CUT&TAG data.
benchmarking encode epigenomics histone-modifications
Last synced: 03 Apr 2025
https://github.com/neurogenomics/benchmark_with_epicompare
ENCODE reproducibility check, cutandrun & TIP-seq benchmark
benchmarking encode epigenomics
Last synced: 03 Apr 2025
https://github.com/andrewdavidsmith/mxe
Methylome transfer engine (mxe)
bisulfite bisulfite-sequencing dna-methylation epigenetics epigenomics methyl-seq methylation methylation-analysis methylome wgbs
Last synced: 29 Nov 2024