methylPipe: Base resolution DNA methylation data analysis

Memory efficient analysis of base resolution DNA methylation data in both the CpG and non-CpG sequence context. Integration of DNA methylation data derived from any methodology providing base- or low-resolution data.

AuthorKamal Kishore
Date of publicationNone
MaintainerKamal Kishore <kamal.fartiyal84@gmail.com>
LicenseGPL(>=2)
Version1.8.0

View on Bioconductor

Functions

binC Man page
binC,GEcollection-method Man page
binmC Man page
binmC,GEcollection-method Man page
binrC Man page
binrC,GEcollection-method Man page
binscore Man page
binscore<- Man page
binscore<-,GEcollection-method Man page
binscore,GEcollection-method Man page
BSdata Man page
BSdata-class Man page
BSdataSet Man page
$,BSdataSet Man page
[,BSdataSet,ANY,ANY-method Man page
[[<-,BSdataSet,ANY,ANY-method Man page
[[,BSdataSet,ANY,ANY-method Man page
BSdataSet-class Man page
$,BSdataSet-method Man page
BSprepare Man page
chiCombP Man page
chr Man page
chr,GEcollection-method Man page
consolidateDMRs Man page
extractBinGRanges Man page
findDMR Man page
findDMR,BSdataSet-method Man page
findDMR-methods Man page
findDMR,methylPipe,BSdataSet Man page
findDMR,methylPipe,BSdataSet-method Man page
findPMDs Man page
findPMDs,BSdata-method Man page
findPMDs-methods Man page
findPMDs,methylPipe,BSdata Man page
findPMDs,methylPipe,BSdata-method Man page
GEcollection Man page
GEcollection-class Man page
GElist Man page
$,GElist Man page
[,GElist,ANY,ANY-method Man page
[[<-,GElist,ANY,ANY-method Man page
[[,GElist,ANY,ANY-method Man page
GElist-class Man page
$,GElist-method Man page
getCpos Man page
getCposChr Man page
getCposDensity Man page
length Man page
length,BSdataSet-method Man page
length,GEcollection-method Man page
length,GElist-method Man page
mapBSdata2GRanges Man page
mapBSdata2GRangesBin Man page
mCsmoothing Man page
mCsmoothing,BSdata-method Man page
mCsmoothing-methods Man page
mCsmoothing,methylPipe,BSdata Man page
mCsmoothing,methylPipe,BSdata-method Man page
meth.call Man page
methstats Man page
methstats,BSdataSet-method Man page
methstats-methods Man page
methstats,methylPipe,BSdataSet Man page
methstats,methylPipe,BSdataSet-method Man page
methylPipe Man page
methylPipe-package Man page
nbins Man page
nbins,GEcollection-method Man page
plotMeth Man page
pool.reads Man page
process.hmc Man page
profileDNAmetBin Man page
profileDNAmetBinParallel Man page
show,BSdata-method Man page
show,BSdataSet-method Man page
show,GEcollection-method Man page
show,GElist-method Man page
splitChrs Man page
tabixdata2GR Man page

Files

methylPipe/DESCRIPTION
methylPipe/NAMESPACE
methylPipe/NEWS
methylPipe/R
methylPipe/R/AllClasses.R methylPipe/R/Allfunctions.R methylPipe/R/BSdata-methods.R methylPipe/R/BSdataSet-methods.R methylPipe/R/GEcollection-methods.R methylPipe/R/GElist-methods.R methylPipe/R/zzz.R
methylPipe/build
methylPipe/build/vignette.rds
methylPipe/exec
methylPipe/exec/methinfo.pl
methylPipe/exec/pool_reads.py
methylPipe/inst
methylPipe/inst/CITATION
methylPipe/inst/doc
methylPipe/inst/doc/methylPipe.R
methylPipe/inst/doc/methylPipe.pdf
methylPipe/inst/doc/methylPipe.rnw
methylPipe/inst/extdata
methylPipe/inst/extdata/DMRs.Rdata
methylPipe/inst/extdata/GR_chr20.Rdata
methylPipe/inst/extdata/H1_chr20_CG_10k.txt
methylPipe/inst/extdata/H1_chr20_CG_10k_tabix_out.txt.gz
methylPipe/inst/extdata/H1_chr20_CG_10k_tabix_out.txt.gz.tbi
methylPipe/inst/extdata/IMR90_chr20_CG_10k_tabix_out.txt.gz
methylPipe/inst/extdata/IMR90_chr20_CG_10k_tabix_out.txt.gz.tbi
methylPipe/inst/extdata/gec.H1.Rdata
methylPipe/inst/extdata/gec.IMR90.Rdata
methylPipe/inst/extdata/test_methcall
methylPipe/inst/extdata/test_methcall/methylPipe_ex.sam
methylPipe/inst/extdata/uncov_GR.Rdata
methylPipe/man
methylPipe/man/BSdata-class.Rd methylPipe/man/BSdataSet-class.Rd methylPipe/man/BSprepare.Rd methylPipe/man/GEcollection-class.Rd methylPipe/man/GElist-class.Rd methylPipe/man/chiCombP.Rd methylPipe/man/consolidateDMRs.Rd methylPipe/man/extractBinGRanges.Rd methylPipe/man/findDMR.Rd methylPipe/man/findPMDs.Rd methylPipe/man/getCpos.Rd methylPipe/man/getCposDensity.Rd methylPipe/man/mCsmoothing.Rd methylPipe/man/mapBSdata2GRanges.Rd methylPipe/man/meth.call.Rd methylPipe/man/methstats.Rd methylPipe/man/methylPipe-package.Rd methylPipe/man/plotMeth.Rd methylPipe/man/pool.reads.Rd methylPipe/man/process.hmc.Rd methylPipe/man/profileDNAmetBin.Rd methylPipe/man/splitChrs.Rd methylPipe/man/tabixdata2GR.Rd
methylPipe/src
methylPipe/src/R_init_methylPipe.c
methylPipe/src/binning.c
methylPipe/src/binning.h
methylPipe/vignettes
methylPipe/vignettes/methylPipe.rnw

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

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