methylPipe: Base resolution DNA methylation data analysis

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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.

Author
Kamal Kishore
Date of publication
None
Maintainer
Kamal Kishore <kamal.fartiyal84@gmail.com>
License
GPL(>=2)
Version
1.8.0

View on Bioconductor

Man pages

BSdata-class
Class "BSdata"
BSdataSet-class
Class "BSdataSet"
BSprepare
Preparing tabular data to be used to feed a BSdata object
chiCombP
Fisher's method implementation
consolidateDMRs
Consolidating Differentially Methylated Regions (DMRs)
extractBinGRanges
Extract genomic ranges for a given bin
findDMR
Identifying Differentially Methylated Regions (DMRs)
findPMDs
Identifying Partially Methylated Domains (PMDs)
GEcollection-class
Class "GEcollection"
GElist-class
Class "GElist"
getCpos
Get genomic Cxx positons for a series of genomic regions
getCposDensity
Determines the density of genomic Cxx positions for a series...
mapBSdata2GRanges
Retrieve mC calls for a GRanges set of genomic regions given...
mCsmoothing
Smoothing and plotting methylation data
meth.call
Function to read methylation calls
methstats
Exploratory statistics of samples in BSdataSet object
methylPipe-package
Analysis of base-pair resolution DNA methylation data.
plotMeth
Plot DNA methylation together with other omics, or annotation...
pool.reads
Function to pool reads of replicates
process.hmc
Processing hmC information from the MLML output
profileDNAmetBin
Profile DNA methylation data for a set of genomic regions
splitChrs
Partitioning genome in chunks, for parallel computation
tabixdata2GR
Convert the list returned by the function scanTabix into a...

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