methylKit: DNA methylation analysis from high-throughput bisulfite sequencing results

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methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Perl is needed to read SAM files only.

Author
Altuna Akalin [aut, cre], Matthias Kormaksson [aut], Sheng Li [aut], Arsene Wabo [ctb], Adrian Bierling [aut], Alexander Gosdschan [aut]
Date of publication
None
Maintainer
Altuna Akalin <aakalin@gmail.com>
License
Artistic-2.0
Version
1.0.0
URLs

View on Bioconductor

Man pages

adjustMethylC
Adjust measured 5mC levels using 5hmC levels
assocComp-methods
Associate principal components with sample annotations
bedgraph-methods
Get bedgraph from methylRaw, methylRawList and methylDiff...
calculateDiffMethDSS-methods
calculate Differential Methylation with DSS
calculateDiffMeth-methods
Calculate differential methylation statistics
clusterSamples-methods
Hierarchical Clustering using methylation data The function...
dataSim-methods
Simulate DNA methylation data
diffMethPerChr-methods
Get and plot the number of hyper/hypo methylated...
extract-methods
extract parts of...
filterByCoverage-methods
Filter methylRaw, methylRawDB, methylRawList and...
genomation-deprecated
Deprecated/Defunct functions
getAssembly-methods
get assembly of the genome
getContext-methods
get the context of methylation
getCorrelation-methods
get correlation between samples in methylBase or methylBaseDB...
getCoverageStats-methods
get coverage stats from methylRaw object
getData-methods
get the data slot from the methylKit objects
getDBPath-methods
Get path to database of the methylDB objects
getMethylationStats-methods
get Methylation stats from methylRaw or methylRawDB object
getMethylDiff-methods
get differentially methylated regions/bases based on cutoffs
getSampleID-methods
Get or Set Sample-IDs of the methylKit objects
getTreatment-methods
Get or Set treatment vector of methylKit object
makeMethylDB-methods
coerce methylKit objects from memory to flat file database...
methRead-methods
read file(s) to methylRaw or methylRawList objects
methSeg
Segment methylation or differential methylation profile
methSeg2bed
Export segments to BED files
methylBase-class
An S4 class for methylation events sampled in multiple...
methylBaseDB-class
An S4 class for storing methylation events sampled in...
methylBase.obj
Example methylBase object.
methylDiff-class
An S4 class that holds differential methylation information
methylDiffDB-class
An S4 class that holds differential methylation information...
methylDiff.obj
Example methylKit objects.
methylRaw-class
An S4 class for holding raw methylation data from an...
methylRawDB-class
An S4 class for storing raw methylation data as flat file...
methylRawList-class
An S4 class for holding a list of methylRaw objects.
methylRawListDB-class
An S4 class for holding a list of methylRawDB objects.
methylRawList.obj
Example methylRawList object.
normalizeCoverage-methods
normalize read coverage between samples
PCASamples-methods
Principal Components Analysis of Methylation data
percMethylation-methods
get percent methylation scores from methylBase or...
pool-methods
Pool replicates within groups to a single sample per group
processBismarkAln-methods
Get methylation percentage from sorted Bismark alignments
reconstruct-methods
Reconstruct methylBase or methylBaseDB object based on a new...
regionCounts
Get regional counts for given GRanges or GRangesList object
removeComp-methods
Remove principal components from a methylBase object
reorganize-methods
Reorganize methylKit objects by creating new objects from...
selectByOverlap-methods
selects records of methylDB objects lying inside a GRanges...
select-methods
selects rows from of methylKit objects
show-methods
show method for methylKit classes
tileMethylCounts-methods
Get methylated/unmethylated base counts for tilling windows
unite-methods
unite methylRawList to a single table
updateMethObject
update methylKit objects The method updates object from...

Files in this package

methylKit/.Rinstignore
methylKit/DESCRIPTION
methylKit/NAMESPACE
methylKit/NEWS
methylKit/R
methylKit/R/RcppExports.R
methylKit/R/adjust.methylC.R
methylKit/R/backbone.R
methylKit/R/batchControl.R
methylKit/R/bedgraph.R
methylKit/R/clusterSamples.R
methylKit/R/dataSim.R
methylKit/R/deprecated_defunct.R
methylKit/R/diffMeth.R
methylKit/R/diffMethDSS.R
methylKit/R/document_data.R
methylKit/R/methSeg.R
methylKit/R/methylDBClasses.R
methylKit/R/methylDBFunctions.R
methylKit/R/methylKit.R
methylKit/R/normalizeCoverage.R
methylKit/R/percMethylation.R
methylKit/R/pool.R
methylKit/R/processBismarkAln.R
methylKit/R/regionalize.R
methylKit/R/reorganize.R
methylKit/R/tabix.functions.R
methylKit/R/updateMethObject.R
methylKit/README.md
methylKit/build
methylKit/build/vignette.rds
methylKit/data
methylKit/data/methylKit.RData
methylKit/inst
methylKit/inst/CITATION
methylKit/inst/doc
methylKit/inst/doc/methylKit.R
methylKit/inst/doc/methylKit.Rmd
methylKit/inst/doc/methylKit.html
methylKit/inst/extdata
methylKit/inst/extdata/control1.myCpG.txt
methylKit/inst/extdata/control2.myCpG.txt
methylKit/inst/extdata/cpgi.hg18.bed.txt
methylKit/inst/extdata/ctrl1.txt.bgz
methylKit/inst/extdata/ctrl2.txt.bgz
methylKit/inst/extdata/generic1.CpG.txt
methylKit/inst/extdata/refseq.hg18.bed.txt
methylKit/inst/extdata/test.fastq_bismark.sorted.min.sam
methylKit/inst/extdata/test.fastq_bismark.unsorted.min.sam
methylKit/inst/extdata/test1.myCpG.txt
methylKit/inst/extdata/test1.txt.bgz
methylKit/inst/extdata/test1_test2_ctrl1_ctrl2.txt.bgz
methylKit/inst/extdata/test1_test2_ctrl1_ctrl2_diffMeth.txt.bgz
methylKit/inst/extdata/test2.myCpG.txt
methylKit/inst/extdata/test2.txt.bgz
methylKit/inst/scripts
methylKit/inst/scripts/create.data.R
methylKit/man
methylKit/man/PCASamples-methods.Rd
methylKit/man/adjustMethylC.Rd
methylKit/man/assocComp-methods.Rd
methylKit/man/bedgraph-methods.Rd
methylKit/man/calculateDiffMeth-methods.Rd
methylKit/man/calculateDiffMethDSS-methods.Rd
methylKit/man/clusterSamples-methods.Rd
methylKit/man/dataSim-methods.Rd
methylKit/man/diffMethPerChr-methods.Rd
methylKit/man/extract-methods.Rd
methylKit/man/filterByCoverage-methods.Rd
methylKit/man/genomation-deprecated.Rd
methylKit/man/getAssembly-methods.Rd
methylKit/man/getContext-methods.Rd
methylKit/man/getCorrelation-methods.Rd
methylKit/man/getCoverageStats-methods.Rd
methylKit/man/getDBPath-methods.Rd
methylKit/man/getData-methods.Rd
methylKit/man/getMethylDiff-methods.Rd
methylKit/man/getMethylationStats-methods.Rd
methylKit/man/getSampleID-methods.Rd
methylKit/man/getTreatment-methods.Rd
methylKit/man/makeMethylDB-methods.Rd
methylKit/man/methRead-methods.Rd
methylKit/man/methSeg.Rd
methylKit/man/methSeg2bed.Rd
methylKit/man/methylBase-class.Rd
methylKit/man/methylBase.obj.Rd
methylKit/man/methylBaseDB-class.Rd
methylKit/man/methylDiff-class.Rd
methylKit/man/methylDiff.obj.Rd
methylKit/man/methylDiffDB-class.Rd
methylKit/man/methylRaw-class.Rd
methylKit/man/methylRawDB-class.Rd
methylKit/man/methylRawList-class.Rd
methylKit/man/methylRawList.obj.Rd
methylKit/man/methylRawListDB-class.Rd
methylKit/man/normalizeCoverage-methods.Rd
methylKit/man/percMethylation-methods.Rd
methylKit/man/pool-methods.Rd
methylKit/man/processBismarkAln-methods.Rd
methylKit/man/reconstruct-methods.Rd
methylKit/man/regionCounts.Rd
methylKit/man/removeComp-methods.Rd
methylKit/man/reorganize-methods.Rd
methylKit/man/select-methods.Rd
methylKit/man/selectByOverlap-methods.Rd
methylKit/man/show-methods.Rd
methylKit/man/tileMethylCounts-methods.Rd
methylKit/man/unite-methods.Rd
methylKit/man/updateMethObject.Rd
methylKit/src
methylKit/src/Makevars
methylKit/src/Makevars.win
methylKit/src/RcppExports.cpp
methylKit/src/methCall.cpp
methylKit/tests
methylKit/tests/testthat
methylKit/tests/testthat.R
methylKit/tests/testthat/test-1-read.r
methylKit/tests/testthat/test-2-unite.r
methylKit/tests/testthat/test-3-clusterSamples.r
methylKit/tests/testthat/test-4-calculateDiffMeth.r
methylKit/tests/testthat/test-5-read.bismark.r
methylKit/tests/testthat/test-6-regionCounts.r
methylKit/tests/testthat/test-7-dataSim.r
methylKit/tests/testthat/test-8-calculateDiffMethDSS.r
methylKit/tests/testthat/test-8-methSeg.r
methylKit/tests/testthat/test-9-tidyUp.r
methylKit/vignettes
methylKit/vignettes/Sweavel.sty
methylKit/vignettes/Vignette_methylKit.bib
methylKit/vignettes/methylKit.Rmd