Last data update: 2014.03.03
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REDseq
Package: REDseq
Type: Package
Title: Analysis of high-throughput sequencing data processed by
restriction enzyme digestion
Version: 1.18.0
Date: 2013-10-21
Author: Lihua Julie Zhu and Thomas Fazzio
Maintainer: Lihua Julie Zhu <julie.zhu@umassmed.edu>
Depends: R (>= 2.15.0), BiocGenerics (>= 0.1.0),
BSgenome.Celegans.UCSC.ce2, multtest, Biostrings, BSgenome,
ChIPpeakAnno
Imports: BiocGenerics, AnnotationDbi, Biostrings, ChIPpeakAnno,
graphics, IRanges (>= 1.13.5), multtest, stats, utils
biocViews: Sequencing, SequenceMatching, Preprocessing
Description: The package includes functions to build restriction enzyme cut site (RECS) map, distribute mapped sequences on the map with five different approaches, find enriched/depleted RECSs for a sample, and identify differentially enriched/depleted RECSs between samples.
License: GPL (>=2)
NeedsCompilation: no
Packaged: 2016-05-04 04:03:50 UTC; biocbuild
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'REDseq' ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "IRanges" for requests: %in%
** help
*** installing help indices
converting help for package 'REDseq'
finding HTML links ... done
REDseq-package html
assignSeq2REsite html
binom.test.REDseq html
buildREmap html
compareREDseq html
distanceHistSeq2RE html
example.REDseq html
example.assignedREDseq html
example.map html
plotCutDistribution html
searchPattern html
summarizeByRE html
summarizeBySeq html
writeHits html
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "IRanges" for requests: %in%
* DONE (REDseq)
Making 'packages.html' ... done
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