Last data update: 2014.03.03
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BiSeq
Package: BiSeq
Type: Package
Title: Processing and analyzing bisulfite sequencing data
Version: 1.12.0
Date: 2015-06-18
Author: Katja Hebestreit, Hans-Ulrich Klein
Maintainer: Katja Hebestreit <katjah@stanford.edu>
Depends: R (>= 2.15.2), methods, S4Vectors, IRanges (>= 1.17.24),
GenomicRanges, SummarizedExperiment (>= 0.2.0), Formula
Imports: methods, BiocGenerics, Biobase, S4Vectors, IRanges,
GenomeInfoDb, GenomicRanges, SummarizedExperiment, rtracklayer,
parallel, betareg, lokern, Formula, globaltest
Description: The BiSeq package provides useful classes and functions to
handle and analyze targeted bisulfite sequencing (BS) data such
as reduced-representation bisulfite sequencing (RRBS) data. In
particular, it implements an algorithm to detect differentially
methylated regions (DMRs). The package takes already aligned BS
data from one or multiple samples.
License: LGPL-3
biocViews: Genetics, Sequencing, MethylSeq, DNAMethylation
NeedsCompilation: no
Packaged: 2016-05-04 04:57:47 UTC; biocbuild
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'BiSeq' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'BiSeq'
finding HTML links ... done
BSraw-class html
finding level-2 HTML links ... done
BSrel-class html
DMRs html
annotateGRanges html
betaRegression html
betaResults html
betaResultsNull html
binomLikelihoodSmooth html
clusterSites html
clusterSitesToGR html
compareTwoSamples html
covBoxplots html
covStatistics html
estLocCor html
filterByCov html
filterBySharedRegions html
findDMRs html
globalTest html
limitCov html
logisticRegression html
makeVariogram html
plotBindingSites html
plotMeth html
plotMethMap html
plotSmoothMeth html
predictMeth html
predictedMeth html
promoters html
rawToRel html
readBismark html
rrbs html
smoothVariogram html
summarizeRegions html
testClusters html
trimClusters html
vario html
writeBED html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BiSeq)
Making 'packages.html' ... done
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