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 <email@example.com>|
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...