bsseq: Analyze, manage and store bisulfite sequencing data

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

Author
Kasper Daniel Hansen [aut, cre], Peter Hickey [ctb]
Date of publication
None
Maintainer
Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
License
Artistic-2.0
Version
1.10.0
URLs

View on Bioconductor

Man pages

BS.chr22
Whole-genome bisulfite sequencing for chromosome 22 from...
BSmooth
BSmooth, smoothing bisulfite sequence data
BSmooth.fstat
Compute F-statistics based on smoothed whole-genome bisulfite...
BSmooth.tstat
Compute t-statistics based on smoothed whole-genome bisulfite...
BSseq
The constructor function for BSseq objects.
BSseq-class
Class BSseq
BSseqStat-class
Class BSseqStat
BSseqTstat-class
Class BSseqTstat
computeStat
Compute a test statistic based on smoothed whole-genome...
data.frame2GRanges
Converts a data frame to a GRanges.
dmrFinder
Finds differentially methylated regions for whole genome...
fisherTests
Compute Fisher-tests for a BSseq object
getCoverage
Obtain coverage for BSseq objects.
getMeth
Obtain methylation estimates for BSseq objects.
getStats
Obtain statistics from a BSseqTstat object
goodnessOfFit
Binomial and poisson goodness of fit statistics for BSSeq...
hasGRanges-class
Class hasGRanges
internals
Internals
plotRegion
Plotting BSmooth methylation estimates
read.bismark
Parsing output from the Bismark alignment suite.
read.bsmooth
Parsing output from the BSmooth alignment suite
read.umtab
Parsing UM tab files (legacy output) containing output from...
smoothSds
Smooth the standard deviations using a thresholded running...

Files in this package

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