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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("methylPipe")
AuthorKamal Kishore
Bioconductor views Coverage DNAMethylation MethylSeq Sequencing
Date of publicationNone
MaintainerKamal Kishore <kamal.fartiyal84@gmail.com>
LicenseGPL(>=2)
Version1.10.0

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

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

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

Please suggest features or report bugs with the GitHub issue tracker.

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