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: 0.99.21
Depends: R (≥ 3.2.0), parallel, GenomicAlignments
Imports: bitops, tools, methods, S4Vectors, IRanges, GenomicRanges, ShortRead, Rsamtools, Biostrings, gtools, rtracklayer, GenomeInfoDb
Published: 2016-03-18
Author: Romain Fenouil, Nicolas Descostes, Lionel Spinelli, Frederic Koch, Muhammad Ahmad Maqbool, Touati Benoukraf, Pierre Cauchy, Charlene Innocenti, Pierre Ferrier, Jean-Christophe Andrau
Maintainer: Romain Fenouil <romain.fenouil at mssm.edu>
License: GPL-3
NeedsCompilation: yes
Materials: NEWS
CRAN checks: Pasha results

Downloads:

Reference manual: Pasha.pdf
Vignettes: Pasha package overview
Package source: Pasha_0.99.21.tar.gz
Windows binaries: r-devel: Pasha_0.99.21.zip, r-release: Pasha_0.99.21.zip, r-oldrel: Pasha_0.99.21.zip
OS X Mavericks binaries: r-release: Pasha_0.99.21.tgz, r-oldrel: Pasha_0.99.21.tgz
Old sources: Pasha archive

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