chromatin-accessibiity

There are 25 repositories under chromatin-accessibiity topic.

  • nf-core/atacseq

    ATAC-seq peak-calling and QC analysis pipeline

    Language:Nextflow180144150116

  • wbaopaul/scATAC-pro

    A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data

    Language:R6966524

  • kundajelab/ChromDragoNN

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

    Language:Jupyter Notebook447711

  • SUwonglab/PECA

    PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data

    Language:MATLAB425146

  • WeiqiangZhou/BIRD

    Big data Regression for predicting DNase I hypersensitivity

    Language:C++293105

  • pinellolab/pychromVAR

    A python package for chromVAR

    Language:Python26142

  • jeongdo801/scNOVA

    scNOVA : Single-Cell Nucleosome Occupancy and genetic Variation Analysis

    Language:R9113

  • Yin-Shen/CharPlant

    A de novo prediction tool of chromatin accessible regions for plant genomes

    Language:Python7201

  • nolan-h-hamilton/ROCCO

    Robust Open Chromatin Detection via Convex Optimization: Multisample Consensus Peak Calling

    Language:Python5200

  • durenzn/PECA

    PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data

    Language:MATLAB4120
  • 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:HTML4192

  • Krebslabrep/Kreibich_2023_5mC_at_enhancers

    Analysis of Single Molecule Footprinting (SMF) data for the analysis of DNA methylation, chromatin accessibility and TF binding. The repository contains all primary code to reproduce the main analyses for the publication "Single molecule footprinting identifies context-dependent regulation of enhancers by DNA methylation" (Kreibich et al., 2023)

    Language:R4000

  • drpatelh/nf-core-atacseq

    See the main fork of this repository here >>>

    Language:Nextflow3120

  • sebastian-gregoricchio/snakeATAC

    Snakemake pipeline for analysis and normalization of ATAC-seq data starting from fastq.gz files.

    Language:Python20

  • UcarLab/BiFET

    A robust statistical test for TF footprint data analyses

    Language:R2452

  • Yin-Shen/CharID

    A two-step model that combines neural network and ensemble learning to predict OCR–mediated interactions.

    Language:Python2102

  • jawa23bio/ATAC-Seq

    Comprehensive analysis pipeline for ATAC-seq data including QC, alignment, peak calling, annotation, motif analysis, and gene enrichment. Delivers key insights and reproducible results for chromatin accessibility studies.

    Language:HTML1100

  • jkmckenna/smftools

    Single Molecule Footprinting Analysis in Python

    Language:Python1200

  • LupienLab/pipeline-chromatin-accessibility

    Instructions on how to perform chromatin accessibility data pre-processing and analyses (focusing on bulk ATAC-seq)

    Language:Python1300

  • tacazares/scATAC_analysis

    A crash course in scATAC-seq data processing

    Language:Python1300

  • bsaintjo/cawlr-rs

    Tool to analyze chromatin accessibility with long read sequencing technologies

    Language:Jupyter Notebook0101

  • DarkAdin/RNAseq-ATACseq

    scRNA-seq and scATAC-seq utilities

    Language:R0100

  • jlduan/cardiomyopathy-etiology

    Rapid diagnostic strategy for cardiomyopathy etiology

    0100

  • StathopoulosLab/Stathopoulos_Lab_Pipelines

    A comprehensive source for Stathopoulos lab code generated and used in data analysis.

    Language:Shell0100

  • WENDYYCM/SAMOSA_ZMW_Selector_Script

    Enhanced zmw_selector.py + New run_zmw_selector.sh

    Language:Python10