Pasha: Preprocessing of Aligned Sequences from HTS Analyses

Pipeline and additional tools designed to handle aligned data from chromatin NGS experiments (less adapted for typical RNAseq applications). Specifically, starting from aligned reads after sequencing, the pipeline function aims at removing artefacts from datasets, estimate in-silico the fragments size, and generate WIG files with corrected values. The package also provides several tools for WIG files manipulations, scaling, merging and subtract (e.g. input).

Version: 0.99.18
Depends: R (≥ 3.2.0), parallel, GenomicAlignments
Imports: bitops, tools, methods, S4Vectors, IRanges, GenomicRanges, ShortRead, Rsamtools, Biostrings, gtools
Published: 2015-10-16
Author: Romain Fenouil, Nicolas Descostes, Lionel Spinelli, Jean-Christophe Andrau
Maintainer: Romain Fenouil <romain.fenouil at>
License: GPL-3
NeedsCompilation: yes
Materials: NEWS
CRAN checks: Pasha results


Reference manual: Pasha.pdf
Vignettes: Pasha package overview
Package source: Pasha_0.99.18.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel: not available
OS X Snow Leopard binaries: r-release: not available, r-oldrel: not available
OS X Mavericks binaries: r-release: Pasha_0.99.18.tgz
Old sources: Pasha archive