Last data update: 2014.03.03

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

● BiocViews: Preprocessing, SequenceMatching, Sequencing
6 images, 11 functions, 3 datasets
● Reverse Depends: 0

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