epigenetics
There are 152 repositories under epigenetics topic.
jts/nanopolish
Signal-level algorithms for MinION data
r3fang/SnapATAC
Analysis Pipeline for Single Cell ATAC-seq
liulab-dfci/MAESTRO
Single-cell Transcriptome and Regulome Analysis Pipeline
BIMSBbioinfo/janggu
Deep learning infrastructure for genomics
nanoporetech/tombo
Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.
YuLab-SMU/ChIPseeker
:dart: ChIP peak Annotation, Comparison and Visualization
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.
cangermueller/deepcpg
Deep neural networks for predicting CpG methylation
yupenghe/methylpy
WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
bioinfomaticsCSU/deepsignal
Detecting methylation using signal-level features from Nanopore sequencing reads
caleblareau/mgatk
mgatk: mitochondrial genome analysis toolkit
kdkorthauer/dmrseq
R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing
pinellolab/haystack_bio
Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
kundajelab/ChromDragoNN
Code for the paper "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts"
epigen/MrBiomics
MrBiomics: Modules & Recipes augment Bioinformatics for Multi-Omics Analyses
caleblareau/gchromVAR
Cell type specific enrichments using finemapped variants and quantitative epigenetic data
liguowang/cpgtools
Python package to analyze DNA methylation data
Larrycpan/MAAS
Delineation of tumor cell subpopulations using MAAS
aryeelab/hichipper
A preprocessing and QC pipeline for HiChIP data
FoxoTech/methylprep
Python-based preprocessing software for Illumina methylation arrays
caleblareau/bap
Bead-based single-cell atac processing
ComputationalAgingLab/ComputAge
A library for full-stack aging clocks design and benchmarking.
AkshajD/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.
tiagochst/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
andreaskapou/BPRMeth
Modelling DNA methylation profiles
deeptools/HiCBrowser
Simple web browser to visualize HiC tracks
datirium/workflows
CWL based Bioinformatics Workflows
eblancoga/seqcode
Suite of command-line software for high-performance graphical analysis of ChIP-seq/RNA-seq/ATAC-seq data
neurogenomics/EpiCompare
Comparison, benchmarking & QC of epigenetic datasets
GryderArt/AQuA-HiChIP
Bioinformatic tools (R scripts) for the analysis of Absolute Quantification of Architecture (AQuA-HiChIP) style data.
fei0810/Triti-Map
A Snakemake-based pipeline for gene mapping in Triticeae.
aldringsvitenskap/epigeneticclock
Calculate DNA methylation age using Horvath 2013 method
caleblareau/proatac
Preprocessing pipeline for (sc)ATAC data
jlab-code/AlphaBeta
Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants
fanglab/BEAST
Bacterial Epigenomics Analysis SuiTe
ngs-ai-org/papet
A collection of softwares to handle and model PacBio kinetic signal data and predict epigenetics modifications.