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Journal Article

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


Koch,  Frederic
Dept. of Developmental Genetics (Head: Bernhard G. Herrmann), Max Planck Institute for Molecular Genetics, Max Planck Society;

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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.

Cite as: https://hdl.handle.net/11858/00-001M-0000-002D-4314-3
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