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

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.

AuthorAltuna Akalin [aut, cre], Matthias Kormaksson [aut], Sheng Li [aut], Arsene Wabo [ctb], Adrian Bierling [aut], Alexander Gosdschan [aut]
Date of publicationNone
MaintainerAltuna Akalin <aakalin@gmail.com>
LicenseArtistic-2.0
Version1.0.0
http://code.google.com/p/methylkit/

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.