pgltools 2.2.0 – Paired Genomic Loci Tool Suite

pgltools 2.2.0

:: DESCRIPTION

Pgltools is a genomic arithmetic software suite designed for working with paired-loci genomic data, such as contacts from a Hi-C or ChIA-PET experiment, and utilizes the PGL file format.

::DEVELOPER

frazer Lab, UCSD

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

Pgltools

:: MORE INFORMATION

Citation

Greenwald WW, Li H, Smith EN, Benaglio P, Nariai N, Frazer KA.
Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data.
BMC Bioinformatics. 2017 Apr 7;18(1):207. doi: 10.1186/s12859-017-1621-0. PMID: 28388874; PMCID: PMC5384132.

HMMcopy 0.1.1 – HMM for Detecting Somatic Copy Number alterations in tumour-normal paired Whole Genome Sequencing data

HMMcopy 0.1.1

:: DESCRIPTION

HMMcopy is a suite of tools to make copy number estimations for whole genome data with GC and mappability correction, then segment and classify copy number profiles with a robust Hidden Markov Model. Designed to work with high coverage whole genome HTS data, it can derive copy number estimations from large (~250GB) aligned BAM files in 2 hours on a single core with minimal memory requirements.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows
R package

:: DOWNLOAD

HMMcopy

:: MORE INFORMATION

Citation

G. Ha, A. Roth, D. Lai, A. Bashashati, J. Ding, R. Goya, R. Giuliany, J. Rosner, A. Oloumi, K. Shumansky, S.-F. Chin, G. Turashvili, M. Hirst, C. Caldas, M. A. Marra, S. Aparicio, S. P. Shah.
Integrative analysis of genome-wide loss of heterozygosity and mono-allelic expression at nucleotide resolution reveals disrupted pathways in triple negative breast cancer.
Genome Research 2012 Oct;22(10):1995-2007.

dCoxS – Biological Interpretation of Paired Gene Sets

dCoxS

:: DESCRIPTION

dCoxS (differentially coexpressed gene sets) is a software that identifies the differentially coexpressed gene set pairs between conditions.

::DEVELOPER

SNUBI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows
R package

:: DOWNLOAD

dCoxS

:: MORE INFORMATION

Citation

Sung Bum Cho, Jihun Kim and Ju Han Kim
Identifying Set-wise Differential Co-expression in Gene Expression Microarray Data
BMC Bioinformatics 2009, 10:109 doi:10.1186/1471-2105-10-109