Learn R Programming

R package: bsseq

This is the developer version of Bioconductor package bsseq. Install in R as:

source('http://bioconductor.org/biocLite.R')
useDevel(TRUE)
biocLite('bsseq')

R CMD check results

Software status

Resource:BioconductorTravis CI
Platforms:MultipleLinux
R CMD check (release) (devel)
Test coverage

Copy Link

Version

Version

1.8.2

License

Artistic-2.0

Issues

61

Pull Requests

6

Stars

35

Forks

25

Maintainer

Kasper Daniel Hansen

Last Published

February 15th, 2017

Functions in bsseq (1.8.2)

BSseq

The constructor function for BSseq objects.
BSmooth.fstat

Compute F-statistics based on smoothed whole-genome bisulfite sequencing data.
smoothSds

Smooth the standard deviations using a thresholded running mean based on smoothed whole-genome bisulfite sequencing data.
BSmooth.tstat

Compute t-statistics based on smoothed whole-genome bisulfite sequencing data.
getCoverage

Obtain coverage for BSseq objects.
getStats

Obtain statistics from a BSseqTstat object
BS.chr22

Whole-genome bisulfite sequencing for chromosome 22 from Lister et al.
BSseqStat-class

Class BSseqStat
fisherTests

Compute Fisher-tests for a BSseq object
BSseqTstat-class

Class BSseqTstat
BSseq-class

Class BSseq
hasGRanges-class

Class hasGRanges
read.bsmooth

Parsing output from the BSmooth alignment suite
read.bismark

Parsing output from the Bismark alignment suite.
Internals

Internals
getMeth

Obtain methylation estimates for BSseq objects.
GoodnessOfFit

Binomial and poisson goodness of fit statistics for BSSeq objects
dmrFinder

Finds differentially methylated regions for whole genome bisulfite sequencing data.
read.umtab

Parsing UM tab files (legacy output) containing output from the BSmooth aligner.
data.frame2GRanges

Converts a data frame to a GRanges.
BSmooth

BSmooth, smoothing bisulfite sequence data
plotRegion

Plotting BSmooth methylation estimates
computeStat

Compute a test statistic based on smoothed whole-genome bisulfite sequencing data.