pint: Pairwise INTegration of functional genomics data

Pairwise data integration for functional genomics, including tools for DNA/RNA/miRNA dependency screens.

AuthorOlli-Pekka Huovilainen <ohuovila@gmail.com> and Leo Lahti <leo.lahti@iki.fi>
Date of publicationNone
MaintainerOlli-Pekka Huovilainen <ohuovila@gmail.com>
LicenseBSD_2_clause + file LICENSE
Version1.24.0
https://github.com/antagomir/pint

View on Bioconductor

Functions

[[ Man page
[[<- Man page
as.data.frame,ChromosomeModels-method Man page
as.data.frame,GenomeModels-method Man page
ChromosomeModels-class Man page
[[<-,ChromosomeModels-method Man page
[[,ChromosomeModels-method Man page
[[,ChromosomeModels-method Man page
dependency score plotting Man page
findModel Man page
findModel,ChromosomeModels-method Man page
findModel,GenomeModels-method Man page
fit.byname Man page
fit.cgh.mir.byname Man page
fit.cgh.mrna.byname Man page
fixed.window Man page
geneCopyNum Man page
GeneDependencyModel-class Man page
geneExp Man page
GenomeModels-class Man page
[[<-,GenomeModels-method Man page
[[,GenomeModels-method Man page
getArm Man page
getArm,ChromosomeModels-method Man page
getArm,GeneDependencyModel-method Man page
getChromosome Man page
getChromosome,ChromosomeModels-method Man page
getChromosome,GeneDependencyModel-method Man page
getGeneName Man page
getGeneName,ChromosomeModels-method Man page
getGeneName,GeneDependencyModel-method Man page
getLoc Man page
getLoc,ChromosomeModels-method Man page
getLoc,GeneDependencyModel-method Man page
getModelMethod Man page
getModelMethod,ChromosomeModels-method Man page
getModelMethod,GenomeModels-method Man page
getModelNumbers Man page
getModelNumbers,ChromosomeModels-method Man page
getModelNumbers,GenomeModels-method Man page
get.neighboring.probes Man page
get.neighs Man page
getParams Man page
getParams,ChromosomeModels-method Man page
getParams,GenomeModels-method Man page
getPArm Man page
getPArm,ChromosomeModels-method Man page
getQArm Man page
getQArm,ChromosomeModels-method Man page
getScore Man page
getScore,ChromosomeModels-method Man page
getScore,GeneDependencyModel-method Man page
getWindowSize Man page
getWindowSize,ChromosomeModels-method Man page
getWindowSize,GeneDependencyModel-method Man page
getWindowSize,GenomeModels-method Man page
getZ,GeneDependencyModel-method Man page
isEmpty Man page
isEmpty,ChromosomeModels-method Man page
isEmpty,ChromosomeModels-method Man page
iterative.window Man page
join.top.regions Man page
order.feature.info Man page
orderGenes Man page
orderGenes,ChromosomeModels-method Man page
orderGenes,GenomeModels-method Man page
pint.data Man page
pint.match Man page
plot.ChromosomeModels Man page
plot.GeneDependencyModel Man page
plot.GenomeModels Man page
screen.cgh.mir Man page
screen.cgh.mrna Man page
setArm<- Man page
setArm<-,GeneDependencyModel-method Man page
setChromosome<- Man page
setChromosome<-,GeneDependencyModel-method Man page
setGeneName<- Man page
setGeneName<-,GeneDependencyModel-method Man page
setLoc<- Man page
setLoc<-,GeneDependencyModel-method Man page
sparse.window Man page
summarize.region.parameters Man page
topGenes Man page
topGenes,ChromosomeModels-method Man page
topGenes,GenomeModels-method Man page
topModels Man page
topModels,ChromosomeModels-method Man page
topModels,GenomeModels-method Man page
W.effects Man page
z.effects Man page

Files

pint/DESCRIPTION
pint/LICENSE
pint/NAMESPACE
pint/R
pint/R/AllClasses.R pint/R/AllGenerics.R pint/R/ChromosomeModels-accessors.R pint/R/GeneDependencyModel-accessors.R pint/R/GenomeModels-accessors.R pint/R/W.effects.R pint/R/calculate.arm.R pint/R/calculate.arm.sparse.R pint/R/calculate.chr.R pint/R/calculate.chr.sparse.R pint/R/calculate.genome.R pint/R/calculate.genome.sparse.R pint/R/centerData.R pint/R/firstlib.R pint/R/fit.cgh.mir.byname.R pint/R/fit.cgh.mrna.byname.R pint/R/fixed.window.R pint/R/imputation.R pint/R/iterative.window.R pint/R/pick.chr.arm.R pint/R/pint.data.R pint/R/pint.match.R pint/R/plot-methods.R pint/R/report.R pint/R/screen.cgh.mir.R pint/R/screen.cgh.mrna.R pint/R/show-methods.R pint/R/sparse.window.R pint/R/test.segmented.R pint/R/z.effects.R
pint/README.md
pint/build
pint/build/vignette.rds
pint/data
pint/data/chromosome17.RData
pint/inst
pint/inst/CITATION
pint/inst/NEWS
pint/inst/doc
pint/inst/doc/depsearch.R
pint/inst/doc/depsearch.Rnw
pint/inst/doc/depsearch.pdf
pint/man
pint/man/ChromosomeModels-class.Rd pint/man/GeneDependencyModel-class.Rd pint/man/GenomeModels-class.Rd pint/man/fit.byname.Rd pint/man/geneCopyNum.Rd pint/man/geneExp.Rd pint/man/get.neighboring.probes.Rd pint/man/get.neighs.Rd pint/man/join.top.regions.Rd pint/man/order.feature.info.Rd pint/man/pint.data.Rd pint/man/plot.Rd pint/man/screen.Rd pint/man/summarize.region.parameters.Rd pint/man/window.Rd pint/man/z.effect.Rd
pint/vignettes
pint/vignettes/cca2.eps
pint/vignettes/cca2.png
pint/vignettes/depsearch-003.eps
pint/vignettes/depsearch-005.eps
pint/vignettes/depsearch.Rnw
pint/vignettes/depsearch.bib

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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All documentation is copyright its authors; we didn't write any of that.