BiSeq: Processing and analyzing bisulfite sequencing data

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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.

Author
Katja Hebestreit, Hans-Ulrich Klein
Date of publication
None
Maintainer
Katja Hebestreit <katjah@stanford.edu>
License
LGPL-3
Version
1.14.0

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