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

Files in this package

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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