Tool to analyze chromatin accessibility with long read sequencing technologies
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Updated
Apr 23, 2024 - Jupyter Notebook
Tool to analyze chromatin accessibility with long read sequencing technologies
Rapid diagnostic strategy for cardiomyopathy etiology
A comprehensive source for Stathopoulos lab code generated and used in data analysis.
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.
Instructions on how to perform chromatin accessibility data pre-processing and analyses (focusing on bulk ATAC-seq)
A crash course in scATAC-seq data processing
A robust statistical test for TF footprint data analyses
A two-step model that combines neural network and ensemble learning to predict OCR–mediated interactions.
Snakemake pipeline for analysis and normalization of ATAC-seq data starting from fastq.gz files.
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.
PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
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)
Robust Open Chromatin Detection via Convex Optimization: Multisample Consensus Peak Calling
A de novo prediction tool of chromatin accessible regions for plant genomes
scNOVA : Single-Cell Nucleosome Occupancy and genetic Variation Analysis
Big data Regression for predicting DNase I hypersensitivity
PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
Code for the paper "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts"
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