Bioinformatic tools (R scripts) for the analysis of Absolute Quantification of Architecture (AQuA-HiChIP) style data.

HiChIP Analysis Tools

Code used to handle CRISPR data and design followup sgRNAs

This repo contains the code used to create the figures and datasets requested by the reviewers of the PAX3-FOXO1/p300 focused Asante et al 2023 paper, submitted to Nature Communications.

R package wrapping bedtools

Components of an automated ChIPseq and ATACseq pipeline

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

Analysis of high-throughput recruitment screens (HT-recruit), from FASTQ to element enrichments.

Accurate and flexible loops calling tool for 3D genomic data.

Preprocesses and Aligns Run-On Sequencing (PRO/GRO/ChRO-seq) data from Single-Read or Paired-End Illumina Sequencing

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

Vennerable provides Venn diagrams in R. It displays Venn and Euler diagrams for up to 9 different sets and using a variety of geometries. It allows the display of area-weighted Venn diagrams and al…

bradner lab computation pipeline scripts