epigenomics
There are 7 repositories under epigenomics topic.
YuLab-SMU / ChIPseeker
:dart: ChIP peak Annotation, Comparison and Visualization
Language:R 222nf-core / methylseq
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
Language:Nextflow 138- Language:R 110
Novartis / peax
Peax is a tool for interactive visual pattern search and exploration in epigenomic data based on unsupervised representation learning with autoencoders
Language:Jupyter Notebook 67pinellolab / haystack_bio
Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
Language:HTML 45- metheor
dohlee / metheor
:comet: Ultrafast DNA methylation heterogeneity calculation from bisulfite alignments (Lee et al., PLOS Computational Biology. 2023)
Language:Rust 43 meuleman / epilogos
Methods for summarizing and visualizing multi-biosample functional genomic annotations
Language:Python 41- cpgtoolsLanguage:Python 38
- Language:Python 37
caleblareau / bap
Bead-based single-cell atac processing
Language:Python 31- chromoformer
The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)
Language:Python 31 - Language:Python 26
broadinstitute / genepy
Genepy is an open source utils package covering a range of useful functions for large scale genomics data analysis in python
Language:Python 20- HuMMuS
cantinilab / HuMMuS
Molecular interactions inference from single-cell multi-omics data
Language:R 19 - Language:R 16
eblancoga / seqcode
Suite of command-line software for high-performance graphical analysis of ChIP-seq/RNA-seq/ATAC-seq data
Language:C 14SchulzLab / EpigenomicsTutorial-ISMB2017
Repository for the Epigenomics Tutorial hold at ISMB 2017 in Prague
Language:Shell 14transbioZI / BioMM
BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data
Language:HTML 14- Language:R 14
hoffmangroup / segway
Application for semi-automated genomic annotation.
Language:Shell 13epifluidlab / FinaleToolkit
FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.
Language:Python 12ma-compbio / GAGE-seq
Data processing and analysis workflow for GAGE-seq, a coassay of single-cell HiC and single-cell RNA-seq
Language:Jupyter Notebook 11- Language:Python 11
- Language:R 10
LieberInstitute / Alzheimers_DNAm
Epigenome-wide analysis of DNA methylation from Alzheimer's patients and unaffected controls
Language:R 9NGSchoolEU / ngs17
Materials used during #NGSchool2017
Language:HTML 9fuxialexander / marvel
Multigranular Analysis of Regulatory Variants on the Epigenomic Landscape
Language:Python 8fungenomics / HGG-oncohistones
Analysis for "K27M in canonical and noncanonical H3 variants occurs in distinct oligodendroglial cell lineages in brain midline gliomas" (Jessa et al, Nature Genetics, 2022)
Language:HTML 6guanjue / IDEAS_2018
Jointly characterizing epigenetic dynamics across multiple cell types
Language:C++ 6- Language:R 6
GabrielHoffman / decorate
Differential Epigenetic Correlation Test
Language:R 5gifford-lab / deepaccess-package
Methods for training and interpretation of an ensemble of neural networks for multi-task functional prediction of accessibility or histone modifications from DNA sequence.
Language:Python 5omics-datascience / multiomix
Multiomix platform source code
Language:TypeScript 5- Language:Red 5
- Language:Python 5
- epiRomics
Huising-Lab / epiRomics
An R package designed to integrate and visualize various levels of epigenomic information, including but not limited to: ChIP, Histone, ATAC, and RNA sequencing. epiRomics is also designed to identify enhancer and enhanceosome regions from these data.
Language:HTML 4
