GitHub topics: chromatin-accessibiity
nf-core/atacseq
ATAC-seq peak-calling and QC analysis pipeline
Language: Nextflow - Size: 9.74 MB - Last synced at: 3 days ago - Pushed at: 2 months ago - Stars: 209 - Forks: 126
jkmckenna/smftools
Single Molecule Footprinting Analysis in Python
Language: Python - Size: 9.04 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 1 - Forks: 0
BesenbacherLab/lionheart
LIONHEART detects cancer from whole genome sequenced plasma cell-free DNA.
Language: Python - Size: 738 KB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 6 - Forks: 1
sdegeorgia/Melanoma_Drug_Resistance_Data
Analysis of gene expression, chromatin accessibility, and resistance phenotypes in melanoma cell lines treated with targeted therapies.
Size: 1000 Bytes - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0
Yin-Shen/CharID
A two-step model that combines neural network and ensemble learning to predict OCR–mediated interactions.
Language: Python - Size: 3.86 MB - Last synced at: 30 days ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 2
nolan-h-hamilton/ROCCO
Robust Open Chromatin Detection via Convex Optimization: Multisample Consensus Peak Calling
Language: Python - Size: 189 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 8 - Forks: 0
dverac/Fiberseq_Nanopore_preprocessing
Pipeline for Pre-processing for Nanopore generated Fiber-seq Data, helps with 5mC and 6mA base modification calling, alignment, phasing and nucleosome calling. This pipeline was designed for the Lab of Sebastian Pott at UC
Language: Python - Size: 200 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0
pinellolab/pychromVAR
A python package for chromVAR
Language: Python - Size: 2.57 MB - Last synced at: 2 months ago - Pushed at: over 2 years ago - Stars: 28 - Forks: 4
LupienLab/pipeline-chromatin-accessibility
Instructions on how to perform chromatin accessibility data pre-processing and analyses (focusing on bulk ATAC-seq)
Language: Python - Size: 52.7 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0
Yin-Shen/CharPlant
A de novo prediction tool of chromatin accessible regions for plant genomes
Language: Python - Size: 553 KB - Last synced at: 30 days ago - Pushed at: about 4 years ago - Stars: 8 - Forks: 1
wbaopaul/scATAC-pro
A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
Language: R - Size: 448 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 74 - Forks: 24
WeiqiangZhou/BIRD
Big data Regression for predicting DNase I hypersensitivity
Language: C++ - Size: 10.9 MB - Last synced at: 4 months ago - Pushed at: about 1 year ago - Stars: 30 - Forks: 5
sebastian-gregoricchio/snakeATAC
Snakemake pipeline for analysis and normalization of ATAC-seq data starting from fastq.gz files.
Language: Python - Size: 4.72 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 0
WENDYYCM/SAMOSA_ZMW_Selector_Script
Enhanced zmw_selector.py + New run_zmw_selector.sh
Language: Python - Size: 10.7 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
tacazares/scATAC_analysis
A crash course in scATAC-seq data processing
Language: Python - Size: 2.12 MB - Last synced at: about 1 year ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 0
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: HTML - Size: 4.91 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0
bsaintjo/cawlr-rs
Tool to analyze chromatin accessibility with long read sequencing technologies
Language: Jupyter Notebook - Size: 209 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 1
kundajelab/ChromDragoNN
Code for the paper "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts"
Language: Jupyter Notebook - Size: 1.27 MB - Last synced at: 10 months ago - Pushed at: about 4 years ago - Stars: 44 - Forks: 11
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: R - Size: 14.1 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 0
SUwonglab/PECA
PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
Language: MATLAB - Size: 19.3 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 38 - Forks: 6
jeongdo801/scNOVA
scNOVA : Single-Cell Nucleosome Occupancy and genetic Variation Analysis
Language: R - Size: 56.6 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 9 - Forks: 3
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 - Size: 32.6 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 2 - Forks: 2
jlduan/cardiomyopathy-etiology
Rapid diagnostic strategy for cardiomyopathy etiology
Size: 58.7 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0
StathopoulosLab/Stathopoulos_Lab_Pipelines
A comprehensive source for Stathopoulos lab code generated and used in data analysis.
Language: Shell - Size: 40 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0
UcarLab/BiFET
A robust statistical test for TF footprint data analyses
Language: R - Size: 1.97 MB - Last synced at: 4 months ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 2
drpatelh/nf-core-atacseq Fork of nf-core/atacseq
See the main fork of this repository here >>>
Language: Nextflow - Size: 7.74 MB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 3 - Forks: 0
