Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)

MNase-seq analysis pipeline using BWA and DANPOS2.

RJMCMC: Genome-Wide Nucleosome Positioning in R

DNAcycP: a deep learning tool for DNA cyclizablity prediction

This R package compares genomic positions and genomic ranges from multiple experiments to extract common regions. The size of the analyzed region is adjustable as well as the number of experiences in which a feature must be present in a potential region to tag this region as a consensus region. Tested on ChIP-Seq peaks and nucleosome positions.

Code for "Comprehensive computational analysis of epigenetic descriptors affecting CRISPR-Cas9 off-target activity"

MNase-seq utilities

Tools to assess the intrinsic nucleosome positioning from sequence information alone

Enhanced zmw_selector.py New run_zmw_selector.sh

Statistical equilibrium models for computing occupancy of nucleosome and transcription-factors.

SRSF framework for nucleosome positioning analysis

This pipeline has been superceeded. Please use >>>

Bioconductor Package - Genome-Wide Nucleosome Positioning in R with an optimized section in C

See the main fork of this repository here >>>