Software Updates

R-pkgs-Biogrids

contains common and requested R packages for BIOGRIDS. This title is dependent on R.

hic_breakfinder

a framework that integrates optical mapping, high-throughput chromosome conformation capture (Hi-C), and whole genome sequencing to systematically detect SVs in a variety of normal or cancer samples and cell lines.

Peakachu

an acronym that standands for Unveil Hi-C Anchors and Peaks, Peakachu takes genome-wide contact data as input and returns coordinates of likely interactions such as chromatin loops.

GATK

(Genome Analysis Toolkit) a software package developed to analyze high-throughput sequencing data capable of taking on projects of any size with a primary focus on variant discovery, genotyping, and data quality assurance.

ITK

(Insight Toolkit) is an open-source, cross-platform library that provides developers with an extensive suite of software tools for image analysis

ExpansionHunter Denovo

(EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs).

DANPOS3

a toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing.