epigenetics
There are 9 repositories under epigenetics topic.
jts / nanopolish
Signal-level algorithms for MinION data
Language:C++ 541- Language:R 295
liulab-dfci / MAESTRO
Single-cell Transcriptome and Regulome Analysis Pipeline
Language:C 261BIMSBbioinfo / janggu
Deep learning infrastructure for genomics
Language:Jupyter Notebook 251nanoporetech / tombo
Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.
Language:Python 220YuLab-SMU / ChIPseeker
:dart: ChIP peak Annotation, Comparison and Visualization
Language:R 205Megalodon 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.
Language:Python 189cangermueller / deepcpg
Deep neural networks for predicting CpG methylation
Language:Python 141- Language:Python 129
bioinfomaticsCSU / deepsignal
Detecting methylation using signal-level features from Nanopore sequencing reads
Language:Python 107caleblareau / mgatk
mgatk: mitochondrial genome analysis toolkit
Language:Python 95kdkorthauer / dmrseq
R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing
Language:R 53kundajelab / ChromDragoNN
Code for the paper "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts"
Language:Jupyter Notebook 44pinellolab / haystack_bio
Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
Language:HTML 43Cell type specific enrichments using finemapped variants and quantitative epigenetic data
Language:R 41- cpgtoolsLanguage:Python 34
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- methylprep
FoxoTech / methylprep
Python-based preprocessing software for Illumina methylation arrays
Language:Python 32 Bead-based single-cell atac processing
Language:Python 31AkshajD / Epigenetic-Clock
This program analyzes methylation levels at six CpG sites in the genome of blood cells to produce a prediction of an individual's biological age, using different machine learning and deep learning models.
Language:Jupyter Notebook 22tiagochst / ELMER
Enhancer Linking by Methylation/Expression Relationship (ELMER) is package to identify tumor-specific changes in DNA methylation within distal enhancers, and link these enhancers to downstream target genes
Language:R 20andreaskapou / BPRMeth
Modelling DNA methylation profiles
Language:R 19deeptools / HiCBrowser
Simple web browser to visualize HiC tracks
Language:JavaScript 17eblancoga / seqcode
Suite of command-line software for high-performance graphical analysis of ChIP-seq/RNA-seq/ATAC-seq data
Language:C 14- Language:Common Workflow Language 13
GryderArt / AQuA-HiChIP
Bioinformatic tools (R scripts) for the analysis of Absolute Quantification of Architecture (AQuA-HiChIP) style data.
Language:R 11neurogenomics / EpiCompare
Comparison, benchmarking & QC of epigenetic datasets
Language:R 11Preprocessing pipeline for (sc)ATAC data
Language:Python 10- Triti-MapLanguage:Python 10
jlab-code / AlphaBeta
Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants
Language:R 10aldringsvitenskap / epigeneticclock
Calculate DNA methylation age using Horvath 2013 method
Language:R 9Bohdan-Khomtchouk / geneXtendeR
R/Bioconductor package for optimized functional annotation of ChIP-seq data
Language:R 9- Language:R 9
giupardeb / EpiMethEx
EpiMethEx (Epigenetic Methylation and Expression), a R package to perform a large-scale integrated analysis by cyclic correlation analyses between methylation and gene expression data.
Language:R 8- Language:Python 8
ngs-ai-org / papet
A collection of softwares to handle and model PacBio kinetic signal data and predict epigenetics modifications.
Language:C++ 8
