title: Pasha: a versatile R package for piling chromatin HTS data.
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.
  
  
  
  Pasha is a multi-platform R package, available on CRAN repositories under GPL-3 license (https://cran.r-project.org/web/packages/Pasha/).
  
  
  
  rfenouil@gmail.com or jean-christophe.andrau@igmm.cnrs.fr
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
authors.forename: Romain
authors.initials: R
authors.lastname: Fenouil
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, New York University Langone School of Medicine, New York, NY, USA.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Descostes
authors.affiliation: Centre D'Immunologie De Marseille-Luminy, Aix Marseille Université UM2, Inserm, U1104, CNRS UMR7280, 13288 Marseille, France.
authors.forename: Lionel
authors.initials: L
authors.lastname: Spinelli
authors.affiliation: Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany.
authors.forename: Frederic
authors.initials: F
authors.lastname: Koch
authors.affiliation: Institute of Molecular Genetics of Montpellier (IGMM), UMR5535 CNRS, 34293 Montpellier, France.
authors.forename: Muhammad Ahmad
authors.initials: MA
authors.lastname: Maqbool
authors.affiliation: Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
authors.forename: Touati
authors.initials: T
authors.lastname: Benoukraf
authors.affiliation: Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK.
authors.forename: Pierre
authors.initials: P
authors.lastname: Cauchy
authors.affiliation: CHU Montpellier, INSERM U1203, Institute of Regenerative Medicine and Biotherapy, Montpellier, France.
authors.forename: Charlène
authors.initials: C
authors.lastname: Innocenti
authors.affiliation: Centre D'Immunologie De Marseille-Luminy, Aix Marseille Université UM2, Inserm, U1104, CNRS UMR7280, 13288 Marseille, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Ferrier
authors.affiliation: Institute of Molecular Genetics of Montpellier (IGMM), UMR5535 CNRS, 34293 Montpellier, France.
authors.forename: Jean-Christophe
authors.initials: JC
authors.lastname: Andrau
mesh_terms: D002843:Chromatin; D059014:High-Throughput Nucleotide Sequencing; D009707:Nucleosomes; D012984:Software
chemical_list: D002843:Chromatin; D009707:Nucleosomes