bsseq: Analyze, manage and store bisulfite sequencing data

A collection of tools for analyzing and visualizing bisulfite sequencing data.

AuthorKasper Daniel Hansen [aut, cre], Peter Hickey [ctb]
Date of publicationNone
MaintainerKasper Daniel Hansen <kasperdanielhansen@gmail.com>
LicenseArtistic-2.0
Version1.10.0
https://github.com/kasperdanielhansen/bsseq

View on Bioconductor

Functions

assayNames,BSseq-method Man page
assays,BSseq-method Man page
binomialGoodnessOfFit Man page
BS.chr22 Man page
BSmooth Man page
BSmooth.fstat Man page
BSmooth.tstat Man page
BSseq Man page
BSseq-class Man page
[,BSseq-method Man page
BSseqStat Man page
[,BSseqStat,ANY,ANY,ANY-method Man page
BSseqStat-class Man page
[,BSseqStat-method Man page
BSseqTstat Man page
[,BSseqTstat,ANY,ANY,ANY-method Man page
BSseqTstat-class Man page
[,BSseqTstat-method Man page
chisqGoodnessOfFit Man page
chrSelectBSseq Man page
collapseBSseq Man page
combine,BSseq,BSseq-method Man page
combineList Man page
computeStat Man page
data.frame2GRanges Man page
dmrFinder Man page
end<-,hasGRanges-method Man page
end,hasGRanges-method Man page
findOverlaps,GenomicRanges,hasGRanges-method Man page
findOverlaps,hasGRanges,GenomicRanges-method Man page
findOverlaps,hasGRanges,hasGRanges-method Man page
fisherTests Man page
getBSseq Man page
getCoverage Man page
getMeth Man page
getStats Man page
granges,hasGRanges-method Man page
hasBeenSmoothed Man page
[,hasGRanges,ANY,ANY,ANY-method Man page
hasGRanges-class Man page
[,hasGRanges-method Man page
length,BSseq-method Man page
length,hasGRanges-method Man page
matrixOrNULL-class Man page
orderBSseq Man page
pData<-,BSseq,data.frame-method Man page
pData<-,BSseq,DataFrame-method Man page
pData,BSseq-method Man page
plot.chisqGoodnessOfFit Man page
plotManyRegions Man page
plotRegion Man page
poissonGoodnessOfFit Man page
poissonGoodnessOfFit Man page
print.chisqGoodnessOfFit Man page
read.bismark Man page
read.bsmooth Man page
read.umtab Man page
read.umtab2 Man page
sampleNames<-,BSseq,ANY-method Man page
sampleNames,BSseq-method Man page
seqlengths<-,hasGRanges-method Man page
seqlengths,hasGRanges-method Man page
seqlevels<-,hasGRanges-method Man page
seqlevels,hasGRanges-method Man page
seqnames<-,hasGRanges-method Man page
seqnames,hasGRanges-method Man page
show,BSseq-method Man page
show,BSseqStat-method Man page
show,BSseqTstat-method Man page
smoothSds Man page
start<-,hasGRanges-method Man page
start,hasGRanges-method Man page
strandCollapse Man page
strand<-,hasGRanges,ANY-method Man page
strand<-,hasGRanges-method Man page
strand,hasGRanges-method Man page
subsetByOverlaps,GenomicRanges,hasGRanges-method Man page
subsetByOverlaps,hasGRanges,GenomicRanges-method Man page
subsetByOverlaps,hasGRanges,hasGRanges-method Man page
updateObject,BSseq-method Man page
width<-,hasGRanges-method Man page
width,hasGRanges-method Man page

Files

bsseq/DESCRIPTION
bsseq/NAMESPACE
bsseq/R
bsseq/R/BSmooth.R bsseq/R/BSmooth.fstat.R bsseq/R/BSmooth.tstat.R bsseq/R/BSseqStat_class.R bsseq/R/BSseqTstat_class.R bsseq/R/BSseq_class.R bsseq/R/BSseq_utils.R bsseq/R/combine.R bsseq/R/dmrFinder.R bsseq/R/fisher.R bsseq/R/getStats.R bsseq/R/gof_stats.R bsseq/R/hasGRanges.R bsseq/R/permutations.R bsseq/R/plotting.R bsseq/R/read.bismark.R bsseq/R/read.bsmooth.R bsseq/R/utils.R
bsseq/README.md
bsseq/build
bsseq/build/vignette.rds
bsseq/data
bsseq/data/BS.chr22.rda
bsseq/data/datalist
bsseq/inst
bsseq/inst/CITATION
bsseq/inst/NEWS.Rd
bsseq/inst/doc
bsseq/inst/doc/bsseq.R
bsseq/inst/doc/bsseq.Rnw
bsseq/inst/doc/bsseq.pdf
bsseq/inst/doc/bsseq_analysis.R
bsseq/inst/doc/bsseq_analysis.Rnw
bsseq/inst/doc/bsseq_analysis.pdf
bsseq/inst/extdata
bsseq/inst/extdata/test_data.cytosineReport.gz
bsseq/inst/extdata/test_data.fastq_bismark.bismark.cov.gz
bsseq/inst/scripts
bsseq/inst/scripts/get_BS.chr22.R
bsseq/inst/unitTests
bsseq/inst/unitTests/test_base.R
bsseq/inst/unitTests/test_perm.R
bsseq/inst/unitTests/test_read.bismark.R
bsseq/man
bsseq/man/BS.chr22.Rd bsseq/man/BSmooth.Rd bsseq/man/BSmooth.fstat.Rd bsseq/man/BSmooth.tstat.Rd bsseq/man/BSseq-class.Rd bsseq/man/BSseq.Rd bsseq/man/BSseqStat-class.Rd bsseq/man/BSseqTstat-class.Rd bsseq/man/computeStat.Rd bsseq/man/data.frame2GRanges.Rd bsseq/man/dmrFinder.Rd bsseq/man/fisherTests.Rd bsseq/man/getCoverage.Rd bsseq/man/getMeth.Rd bsseq/man/getStats.Rd bsseq/man/goodnessOfFit.Rd bsseq/man/hasGRanges-class.Rd bsseq/man/internals.Rd bsseq/man/plotRegion.Rd bsseq/man/read.bismark.Rd bsseq/man/read.bsmooth.Rd bsseq/man/read.umtab.Rd bsseq/man/smoothSds.Rd
bsseq/tests
bsseq/tests/runTests.R
bsseq/vignettes
bsseq/vignettes/bsseq.Rnw
bsseq/vignettes/bsseq.bib
bsseq/vignettes/bsseq_analysis.Rnw
bsseq/vignettes/unsrturl.bst

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.