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

Fenouil, R., Descostes, N., Spinelli, L., Koch, F., Maqbool, M. A., Benoukraf, T., et al. (2016). Pasha: a versatile R package for piling chromatin HTS data. Bioinformatics, 32(16), 2528-2530. doi:10.1093/bioinformatics/btw206.

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2016
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The Author 2016. Published by Oxford University Press. All rights reserved. For
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 Creators:
Fenouil, Romain1, Author
Descostes, Nicolas 2, Author
Spinelli, Lionel3, Author
Koch, Frederic4, Author              
Maqbool, Muhammad Ahmad5, Author
Benoukraf, Touati6, Author
Cauchy, Pierre7, Author
Innocenti , Charlène 8, Author
Ferrier , Pierre 3, Author
Andrau, Jean-Christophe5, Author
Affiliations:
1 Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA., ou_persistent22              
2Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, New York University Langone School of Medicine, , NY, USA., ou_persistent22              
3Centre D’Immunologie De Marseille-Luminy, Aix Marseille Universite ́ , UM2, Inserm, U1104, CNRS UMR7280, 13288 Marseille, France, ou_persistent22              
4Dept. of Developmental Genetics (Head: Bernhard G. Herrmann), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433548              
5Institute of Molecular Genetics of Montpellier (IGMM),, UMR5535 CNRS, 34293 Montpellier, France, ou_persistent22              
6Cancer Science Institute of Singapore, National University of Singapore, ,Singapore, ou_persistent22              
7Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK, ou_persistent22              
8CHU Montpellier, INSERM U1203, Institute of Regenerative Medicine and Biotherapy,, Montpellier, France, ou_persistent22              

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 Abstract: We describe an R package designed for processing aligned reads from chromatin-ori- ented 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 reposito- ries 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 onlin

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 Dates: 2016-04-072015-12-182016-04-082016-04-222016-08-15
 Publication Status: Published in print
 Pages: 3
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 Rev. Type: -
 Identifiers: DOI: 10.1093/bioinformatics/btw206
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Project name : ND was supported by grant from the Ligue Nationale contre le Cancer and MAM by a grant from the ANR iSPLICE
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Funding program : Work in the JCA laboratory is supported by Centre National de la Recherche Scientifique (CNRS), Agence Nationale de la Recherche (ANR), Institut National du Cancer (INCa) and Commission of the European Communities. (ANR-11-BSV8-0013)
Funding organization : -

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Title: Bioinformatics
Source Genre: Journal
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Publ. Info: Oxford : Oxford University Press 32(16):2528-30
Pages: 3 Volume / Issue: 32 (16) Sequence Number: - Start / End Page: 2528 - 2530 Identifier: ISSN: 1367-4803
CoNE: https://pure.mpg.de/cone/journals/resource/954926969991