Format

Send to

Choose Destination
Bioinformatics. 2016 Aug 15;32(16):2528-30. doi: 10.1093/bioinformatics/btw206. Epub 2016 Apr 22.

Pasha: a versatile R package for piling chromatin HTS data.

Author information

1
Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
2
Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, New York University Langone School of Medicine, New York, NY, USA.
3
Centre D'Immunologie De Marseille-Luminy, Aix Marseille Université UM2, Inserm, U1104, CNRS UMR7280, 13288 Marseille, France.
4
Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany.
5
Institute of Molecular Genetics of Montpellier (IGMM), UMR5535 CNRS, 34293 Montpellier, France.
6
Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
7
Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK.
8
CHU Montpellier, INSERM U1203, Institute of Regenerative Medicine and Biotherapy, Montpellier, France.

Abstract

We describe an R package designed for processing aligned reads from chromatin-oriented high-throughput sequencing experiments. Pasha (preprocessing of aligned sequences from HTS analyses) allows easy manipulation of aligned reads from short-read sequencing technologies (ChIP-seq, FAIRE-seq, MNase-Seq, …) and offers innovative approaches such as ChIP-seq reads elongation, nucleosome midpoint piling strategy for positioning analyses, or the ability to subset paired-end reads by groups of insert size that can contain biologically relevant information.

AVAILABILITY AND IMPLEMENTATION:

Pasha is a multi-platform R package, available on CRAN repositories under GPL-3 license (https://cran.r-project.org/web/packages/Pasha/).

CONTACTS:

rfenouil@gmail.com or jean-christophe.andrau@igmm.cnrs.fr

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
27153642
DOI:
10.1093/bioinformatics/btw206
[Indexed for MEDLINE]

Supplemental Content

Full text links

Icon for Silverchair Information Systems
Loading ...
Support Center