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

MNase-seq analysis pipeline using BWA and DANPOS2.

DNAcycP: a deep learning tool for DNA cyclizablity prediction

RJMCMC: Genome-Wide Nucleosome Positioning in R

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.

As a cell-free DNA (cfDNA) processing pipeline, Triton conducts fragmentomic and phased-nucleosome coverage analyses on individual or composite genomic regions and outputs both region-level biomarkers and nt-resolution signal profiles.

MNase-seq utilities

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

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

Enhanced zmw_selector.py + New run_zmw_selector.sh

SRSF framework for nucleosome positioning analysis

Tools to assess the intrinsic nucleosome positioning from sequence information alone

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 >>>