Pasha: a versatile R package for piling chromatin HTS data

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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, …) 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 ( or

Supplementary information: Supplementary data are available at Bioinformatics online.

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