bsseq: Analyze, manage and store bisulfite sequencing data
Version 1.12.1

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

AuthorKasper Daniel Hansen [aut, cre], Peter Hickey [aut]
Bioconductor views DNAMethylation
Date of publicationNone
MaintainerKasper Daniel Hansen <kasperdanielhansen@gmail.com>
LicenseArtistic-2.0
Version1.12.1
URL https://github.com/kasperdanielhansen/bsseq
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("bsseq")

Getting started

README.md

Popular man pages

BSmooth: BSmooth, smoothing bisulfite sequence data
BSmooth.fstat: Compute F-statistics based on smoothed whole-genome bisulfite...
dmrFinder: Finds differentially methylated regions for whole genome...
getMeth: Obtain methylation estimates for BSseq objects.
plotRegion: Plotting BSmooth methylation estimates
read.bismark: Parsing output from the Bismark alignment suite.
read.umtab: Parsing UM tab files (legacy output) containing output from...
See all...

All man pages Function index File listing

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...

Functions

Files

DESCRIPTION
NAMESPACE
R
R/BSmooth.R
R/BSmooth.fstat.R
R/BSmooth.tstat.R
R/BSseqStat_class.R
R/BSseqTstat_class.R
R/BSseq_class.R
R/BSseq_utils.R
R/DelayedArray_utils.R
R/combine.R
R/combine_utils.R
R/dmrFinder.R
R/fisher.R
R/getStats.R
R/gof_stats.R
R/hasGRanges.R
R/hdf5_utils.R
R/permutations.R
R/plotting.R
R/read.bismark.R
R/read.bsmooth.R
R/utils.R
README.md
build
build/vignette.rds
data
data/BS.chr22.rda
data/datalist
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/bsseq.R
inst/doc/bsseq.Rnw
inst/doc/bsseq.pdf
inst/doc/bsseq_analysis.R
inst/doc/bsseq_analysis.Rnw
inst/doc/bsseq_analysis.pdf
inst/extdata
inst/extdata/test_data.cytosineReport.gz
inst/extdata/test_data.fastq_bismark.bismark.cov.gz
inst/scripts
inst/scripts/get_BS.chr22.R
inst/unitTests
inst/unitTests/test_base.R
inst/unitTests/test_combine.R
inst/unitTests/test_hdf5_utils.R
inst/unitTests/test_perm.R
inst/unitTests/test_read.bismark.R
inst/unitTests/test_utils.R
man
man/BS.chr22.Rd
man/BSmooth.Rd
man/BSmooth.fstat.Rd
man/BSmooth.tstat.Rd
man/BSseq-class.Rd
man/BSseq.Rd
man/BSseqStat-class.Rd
man/BSseqTstat-class.Rd
man/computeStat.Rd
man/data.frame2GRanges.Rd
man/dmrFinder.Rd
man/fisherTests.Rd
man/getCoverage.Rd
man/getMeth.Rd
man/getStats.Rd
man/goodnessOfFit.Rd
man/hasGRanges-class.Rd
man/internals.Rd
man/plotRegion.Rd
man/read.bismark.Rd
man/read.bsmooth.Rd
man/read.umtab.Rd
man/smoothSds.Rd
tests
tests/runTests.R
vignettes
vignettes/bsseq.Rnw
vignettes/bsseq.bib
vignettes/bsseq_analysis.Rnw
vignettes/unsrturl.bst
bsseq documentation built on May 20, 2017, 10:37 p.m.

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