bsseq v1.8.2

Analyze, manage and store bisulfite sequencing data

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

Readme

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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Resource: Bioconductor Travis CI
Platforms: Multiple Linux
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Functions in bsseq

Name Description
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.
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Collate hasGRanges.R BSseq_class.R BSseqTstat_class.R BSseq_utils.R combine.R utils.R read.bsmooth.R read.bismark.R BSmooth.R BSmooth.tstat.R dmrFinder.R gof_stats.R plotting.R fisher.R permutations.R BSmooth.fstat.R BSseqStat_class.R getStats.R
License Artistic-2.0
VignetteBuilder knitr
URL https://github.com/kasperdanielhansen/bsseq
LazyData yes
LazyDataCompression xz
BugReports https://github.com/kasperdanielhansen/bsseq/issues
biocViews DNAMethylation

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