{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,23]],"date-time":"2026-01-23T21:44:20Z","timestamp":1769204660171,"version":"3.49.0"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"16","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: 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, \u2026) 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.<\/jats:p>\n               <jats:p>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\/).<\/jats:p>\n               <jats:p>Contacts: \u00a0rfenouil@gmail.com or jean-christophe.andrau@igmm.cnrs.fr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw206","type":"journal-article","created":{"date-parts":[[2016,4,24]],"date-time":"2016-04-24T00:17:47Z","timestamp":1461457067000},"page":"2528-2530","source":"Crossref","is-referenced-by-count":23,"title":["Pasha: a versatile R package for piling chromatin HTS data"],"prefix":"10.1093","volume":"32","author":[{"given":"Romain","family":"Fenouil","sequence":"first","affiliation":[{"name":"1 Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA"}]},{"given":"Nicolas","family":"Descostes","sequence":"additional","affiliation":[{"name":"2 Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, New York University Langone School of Medicine, New York, NY, USA"}]},{"given":"Lionel","family":"Spinelli","sequence":"additional","affiliation":[{"name":"3 Centre D\u2019Immunologie De Marseille-Luminy, Aix Marseille Universit\u00e9 UM2, Inserm, U1104, CNRS UMR7280, 13288 Marseille, France"}]},{"given":"Frederic","family":"Koch","sequence":"additional","affiliation":[{"name":"4 Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany"}]},{"given":"Muhammad Ahmad","family":"Maqbool","sequence":"additional","affiliation":[{"name":"5 Institute of Molecular Genetics of Montpellier (IGMM), UMR5535 CNRS, 34293 Montpellier, France"}]},{"given":"Touati","family":"Benoukraf","sequence":"additional","affiliation":[{"name":"6 Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore"}]},{"given":"Pierre","family":"Cauchy","sequence":"additional","affiliation":[{"name":"7 Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK"}]},{"given":"Charl\u00e8ne","family":"Innocenti","sequence":"additional","affiliation":[{"name":"8 CHU Montpellier, INSERM U1203, Institute of Regenerative Medicine and Biotherapy, Montpellier, France"}]},{"given":"Pierre","family":"Ferrier","sequence":"additional","affiliation":[{"name":"3 Centre D\u2019Immunologie De Marseille-Luminy, Aix Marseille Universit\u00e9 UM2, Inserm, U1104, CNRS UMR7280, 13288 Marseille, France"}]},{"given":"Jean-Christophe","family":"Andrau","sequence":"additional","affiliation":[{"name":"5 Institute of Molecular Genetics of Montpellier (IGMM), UMR5535 CNRS, 34293 Montpellier, France"}]}],"member":"286","published-online":{"date-parts":[[2016,4,22]]},"reference":[{"key":"2023020112533653800_btw206-B1","doi-asserted-by":"crossref","first-page":"e1002111","DOI":"10.1371\/journal.pcbi.1002111","article-title":"Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data","volume":"7","author":"Chung","year":"2011","journal-title":"PLoS Comput. 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