CNOGpro: Copy Numbers of Genes in prokaryotes

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Methods for assigning copy number states and breakpoints in resequencing experiments of prokaryotic organisms.

Author
Ola Brynildsrud, Lars-Gustav Snipen
Date of publication
2015-01-12 23:06:41
Maintainer
Ola Brynildsrud <ola.brynildsrud@nmbu.no>
License
GPL-2
Version
1.1

View on CRAN

Man pages

carsonella
CNV experiment of C. Carsonella ruddy (artificial data)
CNOGpro
Set up a new CNOGpro experiment
CNOGpro-internal
Internal CNOGpro Functions
CNOGpro-package
CNOGpro - Copy Numbers of Genes in Prokaryotes
normalizeGC
Normalization of read count data by GC content
plotCNOGpro
Plots the results of a 'CNOGpro' experiment
printCNOGpro
Prints the results of a 'CNOGpro' experiment
runBootstrap
Gene copy numbers with confidence intervals through...
runHMM
Copy number variation inference through a Hidden Markov Model
store
Store the results of a 'CNOGpro' copy number experiment
summaryCNOGpro
Summarize the 'CNOGpro' experiment

Files in this package

CNOGpro
CNOGpro/inst
CNOGpro/inst/extdata
CNOGpro/inst/extdata/CP003467.gbk
CNOGpro/inst/extdata/carsonellahits.tab
CNOGpro/NAMESPACE
CNOGpro/data
CNOGpro/data/carsonella.rda
CNOGpro/R
CNOGpro/R/calculateProb.R
CNOGpro/R/addState.R
CNOGpro/R/CNOGpro.R
CNOGpro/R/printCNOGpro.R
CNOGpro/R/getsequence.R
CNOGpro/R/updateGeneTable.R
CNOGpro/R/gethits.R
CNOGpro/R/runBootstrap.R
CNOGpro/R/copynumberBootstrap.R
CNOGpro/R/solvePR.R
CNOGpro/R/setupEmissionMatrix.R
CNOGpro/R/normalizeGC.R
CNOGpro/R/CNOGpro-internal.R
CNOGpro/R/store.R
CNOGpro/R/makeViterbimat.R
CNOGpro/R/getGCinwindows.R
CNOGpro/R/setupTransitionMatrix.R
CNOGpro/R/insertRow.R
CNOGpro/R/readGenBank.R
CNOGpro/R/getreadcounts.R
CNOGpro/R/plotCNOGpro.R
CNOGpro/R/getMembership.R
CNOGpro/R/isbetween.R
CNOGpro/R/summaryCNOGpro.R
CNOGpro/R/rgammapois.R
CNOGpro/R/spans.R
CNOGpro/R/HMMcopynumber.R
CNOGpro/R/sampleChromosome.R
CNOGpro/R/runHMM.R
CNOGpro/MD5
CNOGpro/DESCRIPTION
CNOGpro/man
CNOGpro/man/runHMM.Rd
CNOGpro/man/plotCNOGpro.Rd
CNOGpro/man/normalizeGC.Rd
CNOGpro/man/store.Rd
CNOGpro/man/printCNOGpro.Rd
CNOGpro/man/summaryCNOGpro.Rd
CNOGpro/man/CNOGpro-package.Rd
CNOGpro/man/runBootstrap.Rd
CNOGpro/man/carsonella.Rd
CNOGpro/man/CNOGpro.Rd
CNOGpro/man/CNOGpro-internal.Rd