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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')

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Software status

Resource:	Bioconductor	Travis CI
Platforms:	Multiple	Linux
R CMD check	(release) (devel)
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Version

Version

1.8.2

License

Artistic-2.0

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Repository

https://github.com/kasperdanielhansen/bsseq

Maintainer

Kasper Daniel Hansen

Last Published

February 15th, 2017

Functions in bsseq (1.8.2)

The constructor function for BSseq objects.

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

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

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

Obtain coverage for BSseq objects.

Obtain statistics from a BSseqTstat object

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

BSseqStat-class

Class BSseqStat

Compute Fisher-tests for a BSseq object

BSseqTstat-class

Class BSseqTstat

hasGRanges-class

Class hasGRanges

Parsing output from the BSmooth alignment suite

Parsing output from the Bismark alignment suite.

Obtain methylation estimates for BSseq objects.

Binomial and poisson goodness of fit statistics for BSSeq objects

Finds differentially methylated regions for whole genome bisulfite sequencing data.

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

data.frame2GRanges

Converts a data frame to a GRanges.

BSmooth, smoothing bisulfite sequence data

Plotting BSmooth methylation estimates

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