biomvRCNS: Copy Number study and Segmentation for multivariate biological data
Version 1.16.0

In this package, a Hidden Semi Markov Model (HSMM) and one homogeneous segmentation model are designed and implemented for segmentation genomic data, with the aim of assisting in transcripts detection using high throughput technology like RNA-seq or tiling array, and copy number analysis using aCGH or sequencing.

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AuthorYang Du
Bioconductor views CopyNumberVariation Genetics Microarray Sequencing Visualization aCGH
Date of publicationNone
MaintainerYang Du <tooyoung@gmail.com>
LicenseGPL (>= 2)
Version1.16.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("biomvRCNS")

Man pages

biomvRCNS-class: Class '"biomvRCNS"'
biomvRGviz: Plot segmentation result using Gviz
biomvRhsmm: Estimating the most likely state sequence using Hidden Semi...
biomvRmgmr: Batch process multiple sequences and samples using...
biomvRseg: Homogeneous segmentation of multi-sample genomic data
coriell: Array CGH data set of Coriell cell lines
encodeTP53: mapped RNA-seq data from ENCODE
hsmmRun: Estimating the most likely state sequence using Hidden Semi...
maxGapminRun: Max-gap-min-run algorithm for 2 states segmentation
regionSegAlphaNB: Estimate matrix of dispersion parameter alpha (size) used in...
regionSegCost: Regional segmentation cost matrix
simSegData: Simulate exemplary segmentation data.
sojournAnno: Estimate sojourn distribution parameters from posterior...
splitFarNeighbour: Split segments if long gaps exist between feature positions
variosm: Differential methylation data from sequencing

Functions

NBlogL1stTerm Source code
avgFunc Source code
biomvRCNS-class Man page
biomvRGviz Man page Source code
biomvRhsmm Man page Source code
biomvRmgmr Man page Source code
biomvRseg Man page Source code
coriell Man page
encodeTP53 Man page
estEmis Source code
estEmisMu Source code
estEmisVar Source code
estimateSegCommonDisp Source code
gammaFit Source code
hsmmRun Man page Source code
initDposV Source code
initEmis Source code
initSojDd Source code
mat2list Source code
maxGapminRun Man page Source code
nbinomCLLDD Source code
nbinomFit Source code
plot,biomvRCNS,ANY-method Man page
poisFit Source code
preClustGrp Source code
regionSegAlphaNB Man page Source code
regionSegCost Man page Source code
show,biomvRCNS-method Man page
simSegData Man page Source code
simUvSegData Source code
sojournAnno Man page Source code
splitFarNeighbour Man page Source code
splitFarNeighbouryhat Source code
tmvtfFit Source code
unifMJ Source code
variosm Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/biomvRhsmm.R
R/biomvRplot.R
R/biomvRseg.R
R/defClasses.R
R/misc.R
build
build/vignette.rds
data
data/coriell.rda
data/encodeTP53.rda
data/variosm.rda
inst
inst/CITATION
inst/doc
inst/doc/biomvRCNS.R
inst/doc/biomvRCNS.Rnw
inst/doc/biomvRCNS.pdf
inst/extdata
inst/extdata/encodeFiles.txt
inst/extdata/gmodTP53.gff
man
man/biomvRCNS-class.Rd
man/biomvRGviz.Rd
man/biomvRhsmm.Rd
man/biomvRmgmr.Rd
man/biomvRseg.Rd
man/coriell.Rd
man/encodeTP53.Rd
man/hsmmRun.Rd
man/maxGapminRun.Rd
man/regionSegAlphaNB.Rd
man/regionSegCost.Rd
man/simSegData.Rd
man/sojournAnno.Rd
man/splitFarNeighbour.Rd
man/variosm.Rd
src
src/biomvRCNS.c
vignettes
vignettes/biomvRCNS.Rnw
vignettes/biomvRCNS.bib
biomvRCNS documentation built on May 20, 2017, 9:14 p.m.