A robust statistical test for TF footprint data analyses
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Updated
Mar 11, 2020 - R
A robust statistical test for TF footprint data analyses
Code for the paper "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts"
A de novo prediction tool of chromatin accessible regions for plant genomes
A two-step model that combines neural network and ensemble learning to predict OCR–mediated interactions.
A crash course in scATAC-seq data processing
Instructions on how to perform chromatin accessibility data pre-processing and analyses (focusing on bulk ATAC-seq)
PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
A comprehensive source for Stathopoulos lab code generated and used in data analysis.
Big data Regression for predicting DNase I hypersensitivity
A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
scNOVA : Single-Cell Nucleosome Occupancy and genetic Variation Analysis
Rapid diagnostic strategy for cardiomyopathy etiology
PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
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.
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)
Tool to analyze chromatin accessibility with long read sequencing technologies
Snakemake pipeline for analysis and normalization of ATAC-seq data starting from fastq.gz files.
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