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...

Files in this package

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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