biomvRCNS: Copy Number study and Segmentation for multivariate biological data

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.

Author
Yang Du
Date of publication
None
Maintainer
Yang Du <tooyoung@gmail.com>
License
GPL (>= 2)
Version
1.14.0

View on Bioconductor

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

Files in this package

biomvRCNS/DESCRIPTION
biomvRCNS/NAMESPACE
biomvRCNS/NEWS
biomvRCNS/R
biomvRCNS/R/biomvRhsmm.R
biomvRCNS/R/biomvRplot.R
biomvRCNS/R/biomvRseg.R
biomvRCNS/R/defClasses.R
biomvRCNS/R/misc.R
biomvRCNS/build
biomvRCNS/build/vignette.rds
biomvRCNS/data
biomvRCNS/data/coriell.rda
biomvRCNS/data/encodeTP53.rda
biomvRCNS/data/variosm.rda
biomvRCNS/inst
biomvRCNS/inst/CITATION
biomvRCNS/inst/doc
biomvRCNS/inst/doc/biomvRCNS.R
biomvRCNS/inst/doc/biomvRCNS.Rnw
biomvRCNS/inst/doc/biomvRCNS.pdf
biomvRCNS/inst/extdata
biomvRCNS/inst/extdata/encodeFiles.txt
biomvRCNS/inst/extdata/gmodTP53.gff
biomvRCNS/man
biomvRCNS/man/biomvRCNS-class.Rd
biomvRCNS/man/biomvRGviz.Rd
biomvRCNS/man/biomvRhsmm.Rd
biomvRCNS/man/biomvRmgmr.Rd
biomvRCNS/man/biomvRseg.Rd
biomvRCNS/man/coriell.Rd
biomvRCNS/man/encodeTP53.Rd
biomvRCNS/man/hsmmRun.Rd
biomvRCNS/man/maxGapminRun.Rd
biomvRCNS/man/regionSegAlphaNB.Rd
biomvRCNS/man/regionSegCost.Rd
biomvRCNS/man/simSegData.Rd
biomvRCNS/man/sojournAnno.Rd
biomvRCNS/man/splitFarNeighbour.Rd
biomvRCNS/man/variosm.Rd
biomvRCNS/src
biomvRCNS/src/biomvRCNS.c
biomvRCNS/vignettes
biomvRCNS/vignettes/biomvRCNS.Rnw
biomvRCNS/vignettes/biomvRCNS.bib