Package: Pasha
Type: Package
Title: Preprocessing of Aligned Sequences from HTS Analyses
Version: 0.99.21
Date: 2016-03-04
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@mssm.edu>
Description: 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).
License: GPL-3
LazyLoad: yes
Imports: bitops, tools, methods, S4Vectors, IRanges, GenomicRanges,
        ShortRead, Rsamtools, Biostrings, gtools, rtracklayer,
        GenomeInfoDb
Depends: R (>= 3.2.0), parallel, GenomicAlignments
biocViews: ChIPSeq, Sequencing, Software, Preprocessing, Alignment
NeedsCompilation: yes
Packaged: 2016-03-18 15:19:11 UTC; fenouil
Repository: CRAN
Date/Publication: 2016-03-18 16:23:47
Built: R 3.3.2; x86_64-w64-mingw32; 2016-10-31 23:53:41 UTC; windows
Archs: i386, x64
