BiSeq: Processing and analyzing bisulfite sequencing data

The BiSeq package provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data. In particular, it implements an algorithm to detect differentially methylated regions (DMRs). The package takes already aligned BS data from one or multiple samples.

AuthorKatja Hebestreit, Hans-Ulrich Klein
Date of publicationNone
MaintainerKatja Hebestreit <katjah@stanford.edu>
LicenseLGPL-3
Version1.14.0

View on Bioconductor

Man pages

annotateGRanges: Annotates a 'GRanges' object by means of a second 'GRanges'...

betaRegression: A function to estimate and test a group factor within a beta...

betaResults: The output of 'betaRegression'

betaResultsNull: The output of 'betaRegression' for resampled data

binomLikelihoodSmooth: Calculates local likelihood estimations for binomial random...

BSraw-class: Class to contain raw Bisulfite Sequencing (BiSeq) Data

BSrel-class: Class to contain Bisulfite Sequencing (BiSeq) Data

clusterSites: Assigns CpG cluster memberships on CpG sites within 'BSraw'...

clusterSitesToGR: A function to obtain a 'GRanges' object of CpG clusters from...

compareTwoSamples: Detects DMRs by comparing two samples

covBoxplots: Creates boxplots of coverages per sample

covStatistics: Prints a short summary of coverage statistics per sample

DMRs: The output of 'findDMRs'

estLocCor: Estimates the correlations of the z-scores

filterByCov: Filters regions (or single CpGs) of a 'BSraw' object with a...

filterBySharedRegions: Reduces a 'BSraw' or 'BSrel' object to regions (or single...

findDMRs: Aggregates CpG sites to DMRs

globalTest: Test whether at least one CpG is differentially methylated in...

limitCov: Limits the coverage of a 'BSraw' object

logisticRegression: Estimates and tests a group factor

makeVariogram: Variogram estimator.

plotBindingSites: Plots the mean methylation of given regions

plotMeth: Plots raw and smoothed methylation data for a given region

plotMethMap: Plots methylation values of multiple samples in a given...

plotSmoothMeth: Plots smoothed methylation values for a bunch of samples and...

predictedMeth: The output of 'predictMeth'

predictMeth: Predicts methylation levels along CpG sites or for a grid of...

promoters: A 'GRanges' of promoters of the human genome

rawToRel: Converts a 'BSraw' object to a 'BSrel' object

readBismark: Reads cytosine methylation stati determined by Bismark

rrbs: RRBS data of APL patient samples and controls.

smoothVariogram: Smoothes variogram

summarizeRegions: Aggregates methylation information of single CpG sites

testClusters: Tests CpG clusters

trimClusters: Trims CpG clusters

vario: Output of 'makeVariogram'

writeBED: Writes 'BSraw' and 'BSrel' data to a bed file suitable for...

Functions

annotateGRanges Man page
annotateGRanges,GRanges,GRanges,character,character-method Man page
annotateGRanges,GRanges,GRanges,character,integer-method Man page
annotateGRanges,GRanges,GRanges,character,missing-method Man page
betaRegression Man page
betaRegression,formula,character,BSrel,missing-method Man page
betaRegression,formula,character,BSrel,numeric-method Man page
betaResults Man page
betaResultsNull Man page
binomLikelihoodSmooth Man page
binomLikelihoodSmooth,ANY-method Man page
BSraw Man page
BSraw-class Man page
BSraw,matrix,matrix,GRanges-method Man page
BSrel Man page
BSrel-class Man page
BSrel,matrix,GRanges-method Man page
clusterSites Man page
clusterSites,BSraw,ANY,numeric,missing,missing,missing-method Man page
clusterSites,BSraw,ANY,numeric,missing,numeric,missing-method Man page
clusterSites,BSraw,ANY,numeric,numeric,missing,missing-method Man page
clusterSites,BSraw,ANY,numeric,numeric,numeric,missing-method Man page
clusterSites,BSraw,ANY,numeric,numeric,numeric,numeric-method Man page
clusterSites,BSraw,missing,missing,missing,missing,missing-metho Man page
clusterSites,BSraw,missing,numeric,numeric,numeric,missing-metho Man page
clusterSites,BSraw,missing,numeric,numeric,numeric,numeric-metho Man page
clusterSitesToGR Man page
clusterSitesToGR,BSraw-method Man page
clusterSitesToGR,BSrel-method Man page
combine,BSraw,BSraw-method Man page
combine,BSrel,BSrel-method Man page
compareTwoSamples Man page
compareTwoSamples,BSraw,character,character,numeric,numeric-meth Man page
compareTwoSamples,BSraw,numeric,numeric,numeric,numeric-method Man page
compareTwoSamples,BSrel,character,character,numeric,numeric-meth Man page
compareTwoSamples,BSrel,numeric,numeric,numeric,numeric-method Man page
covBoxplots Man page
covBoxplots,BSraw-method Man page
covStatistics Man page
covStatistics,BSraw-method Man page
covStatistics,BSrel-method Man page
DMRs Man page
estLocCor Man page
estLocCor,list-method Man page
filterByCov Man page
filterByCov,BSraw,missing,logical-method Man page
filterByCov,BSraw,missing,missing-method Man page
filterByCov,BSraw,numeric,logical-method Man page
filterByCov,BSraw,numeric,missing-method Man page
filterBySharedRegions Man page
filterBySharedRegions,BSraw,ANY,missing,numeric,missing-method Man page
filterBySharedRegions,BSraw,ANY,missing,numeric,numeric-method Man page
filterBySharedRegions,BSraw,ANY,numeric,missing,missing-method Man page
filterBySharedRegions,BSraw,ANY,numeric,missing,numeric-method Man page
filterBySharedRegions,BSraw,missing,missing,missing,missing-meth Man page
filterBySharedRegions,BSraw,missing,missing,missing,numeric-meth Man page
filterBySharedRegions,BSraw,missing,missing,numeric,missing-meth Man page
filterBySharedRegions,BSraw,missing,missing,numeric,numeric-meth Man page
filterBySharedRegions,BSraw,missing,numeric,missing,missing-meth Man page
filterBySharedRegions,BSraw,missing,numeric,missing,numeric-meth Man page
filterBySharedRegions,BSrel,ANY,missing,numeric,ANY-method Man page
filterBySharedRegions,BSrel,ANY,numeric,missing,ANY-method Man page
filterBySharedRegions,BSrel,missing,missing,missing,ANY-method Man page
filterBySharedRegions,BSrel,missing,missing,numeric,ANY-method Man page
filterBySharedRegions,BSrel,missing,numeric,missing,ANY-method Man page
findDMRs Man page
findDMRs,data.frame,missing,numeric,logical-method Man page
findDMRs,data.frame,missing,numeric,missing-method Man page
findDMRs,data.frame,numeric,numeric,logical-method Man page
findDMRs,data.frame,numeric,numeric,missing-method Man page
globalTest Man page
globalTest,ANY,BSrel-method Man page
limitCov Man page
limitCov,BSraw,numeric-method Man page
logisticRegression Man page
logisticRegression,formula,character,BSrel,missing-method Man page
logisticRegression,formula,character,BSrel,numeric-method Man page
makeVariogram Man page
makeVariogram,data.frame,logical,missing,missing-method Man page
makeVariogram,data.frame,logical,missing,numeric-method Man page
makeVariogram,data.frame,logical,numeric,missing-method Man page
makeVariogram,data.frame,logical,numeric,numeric-method Man page
makeVariogram,data.frame,missing,missing,missing-method Man page
makeVariogram,data.frame,missing,numeric,numeric-method Man page
methLevel Man page
methLevel<- Man page
methLevel<-,BSrel,matrix-method Man page
methLevel,BSrel-method Man page
methReads Man page
methReads<- Man page
methReads<-,BSraw,matrix-method Man page
methReads,BSraw-method Man page
plotBindingSites Man page
plotBindingSites,BSraw,GRanges-method Man page
plotBindingSites,BSrel,GRanges-method Man page
plotMeth Man page
plotMeth,BSraw,BSrel,GRanges-method Man page
plotMethMap Man page
plotMethMap,BSraw,GRanges,factor,logical-method Man page
plotMethMap,BSraw,GRanges,factor,missing-method Man page
plotMethMap,BSraw,GRanges,missing,logical-method Man page
plotMethMap,BSraw,GRanges,missing,missing-method Man page
plotMethMap,BSrel,GRanges,factor,logical-method Man page
plotMethMap,BSrel,GRanges,factor,missing-method Man page
plotMethMap,BSrel,GRanges,missing,logical-method Man page
plotMethMap,BSrel,GRanges,missing,missing-method Man page
plotSmoothMeth Man page
plotSmoothMeth,BSrel,GRanges,ANY,logical-method Man page
plotSmoothMeth,BSrel,GRanges,ANY,missing-method Man page
predictedMeth Man page
predictMeth Man page
predictMeth,BSraw,missing,missing,missing-method Man page
predictMeth,BSraw,missing,missing,numeric-method Man page
predictMeth,BSraw,numeric,missing,missing-method Man page
predictMeth,BSraw,numeric,missing,numeric-method Man page
predictMeth,BSraw,numeric,numeric,numeric-method Man page
promoters Man page
rawToRel Man page
rawToRel,BSraw-method Man page
readBismark Man page
readBismark,character,character-method Man page
readBismark,character,data.frame-method Man page
readBismark,character,DataFrame-method Man page
rrbs Man page
smoothVariogram Man page
smoothVariogram,list,numeric,missing-method Man page
smoothVariogram,list,numeric,numeric-method Man page
smoothVariogram,matrix,numeric,missing-method Man page
smoothVariogram,matrix,numeric,numeric-method Man page
summarizeRegions Man page
summarizeRegions,BSraw,GRanges,logical-method Man page
summarizeRegions,BSraw,GRanges,missing-method Man page
summarizeRegions,BSrel,GRanges,logical-method Man page
summarizeRegions,BSrel,GRanges,missing-method Man page
testClusters Man page
testClusters,list,missing-method Man page
testClusters,list,numeric-method Man page
totalReads Man page
totalReads<- Man page
totalReads<-,BSraw,matrix-method Man page
totalReads,BSraw-method Man page
trimClusters Man page
trimClusters,list,missing-method Man page
trimClusters,list,numeric-method Man page
vario Man page
writeBED Man page
writeBED,BSraw,character,character-method Man page
writeBED,BSraw,character,missing-method Man page
writeBED,BSraw,missing,character-method Man page
writeBED,BSraw,missing,missing-method Man page
writeBED,BSrel,character,character-method Man page
writeBED,BSrel,character,missing-method Man page
writeBED,BSrel,missing,character-method Man page
writeBED,BSrel,missing,missing-method Man page

Files

BiSeq/.BBSoptions
BiSeq/DESCRIPTION
BiSeq/NAMESPACE
BiSeq/R
BiSeq/R/AllClasses.R BiSeq/R/AllGenerics.R BiSeq/R/annotateGRanges.R BiSeq/R/betaRegression.R BiSeq/R/binomLikelihoodSmooth.R BiSeq/R/categorialColors.R BiSeq/R/clusterSites.R BiSeq/R/clusterSitesToGR.R BiSeq/R/compareTwoSamples.R BiSeq/R/covBoxplots.R BiSeq/R/covStatistics.R BiSeq/R/estLocCor.R BiSeq/R/filterByCov.R BiSeq/R/filterBySharedRegions.R BiSeq/R/findDMRs.R BiSeq/R/globalTest.R BiSeq/R/limitCov.R BiSeq/R/logisticRegression.R BiSeq/R/makeVariogram.R BiSeq/R/methods-BSraw.R BiSeq/R/methods-BSrel.R BiSeq/R/plotBindingSites.R BiSeq/R/plotMeth.R BiSeq/R/plotMethMap.R BiSeq/R/plotSmoothMeth.R BiSeq/R/predictMeth.R BiSeq/R/rawToRel.R BiSeq/R/readBismark.R BiSeq/R/smoothVariogram.R BiSeq/R/summarizeRegions.R BiSeq/R/testClusters.R BiSeq/R/trimClusters.R BiSeq/R/variogram.R BiSeq/R/writeBED.R
BiSeq/build
BiSeq/build/vignette.rds
BiSeq/data
BiSeq/data/DMRs.RData
BiSeq/data/betaResults.RData
BiSeq/data/betaResultsNull.RData
BiSeq/data/datalist
BiSeq/data/predictedMeth.RData
BiSeq/data/promoters.RData
BiSeq/data/rrbs.RData
BiSeq/data/vario.RData
BiSeq/inst
BiSeq/inst/doc
BiSeq/inst/doc/BiSeq.R
BiSeq/inst/doc/BiSeq.Rnw
BiSeq/inst/doc/BiSeq.pdf
BiSeq/inst/extdata
BiSeq/inst/extdata/CpG_context_test_sample.cov
BiSeq/man
BiSeq/man/BSraw-class.Rd BiSeq/man/BSrel-class.Rd BiSeq/man/DMRs.Rd BiSeq/man/annotateGRanges.Rd BiSeq/man/betaRegression.Rd BiSeq/man/betaResults.Rd BiSeq/man/betaResultsNull.Rd BiSeq/man/binomLikelihoodSmooth.Rd BiSeq/man/clusterSites.Rd BiSeq/man/clusterSitesToGR.Rd BiSeq/man/compareTwoSamples.Rd BiSeq/man/covBoxplots.Rd BiSeq/man/covStatistics.Rd BiSeq/man/estLocCor.Rd BiSeq/man/filterByCov.Rd BiSeq/man/filterBySharedRegions.Rd BiSeq/man/findDMRs.Rd BiSeq/man/globalTest.Rd BiSeq/man/limitCov.Rd BiSeq/man/logisticRegression.Rd BiSeq/man/makeVariogram.Rd BiSeq/man/plotBindingSites.Rd BiSeq/man/plotMeth.Rd BiSeq/man/plotMethMap.Rd BiSeq/man/plotSmoothMeth.Rd BiSeq/man/predictMeth.Rd BiSeq/man/predictedMeth.Rd BiSeq/man/promoters.Rd BiSeq/man/rawToRel.Rd BiSeq/man/readBismark.Rd BiSeq/man/rrbs.Rd BiSeq/man/smoothVariogram.Rd BiSeq/man/summarizeRegions.Rd BiSeq/man/testClusters.Rd BiSeq/man/trimClusters.Rd BiSeq/man/vario.Rd BiSeq/man/writeBED.Rd
BiSeq/vignettes
BiSeq/vignettes/BiSeq.Rnw
BiSeq/vignettes/BiSeq.bib
BiSeq/vignettes/igv_snapshot.png
BiSeq/vignettes/igv_snapshot_smoothed.png
BiSeq/vignettes/unsrturl.bst

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