gespeR: Gene-Specific Phenotype EstimatoR
Version 1.8.0

Estimates gene-specific phenotypes from off-target confounded RNAi screens. The phenotype of each siRNA is modeled based on on-targeted and off-targeted genes, using a regularized linear regression model.

AuthorFabian Schmich
Bioconductor views CellBasedAssays GeneTarget Preprocessing Regression Visualization
Date of publicationNone
MaintainerFabian Schmich <fabian.schmich@bsse.ethz.ch>
LicenseGPL-3
Version1.8.0
URL http://www.cbg.ethz.ch/software/gespeR
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("gespeR")

Getting started

Package overview
README.md

Popular man pages

as.data.frame-Phenotypes-method: Convert Phenotypes object to a data.frame
c-Phenotypes-method: Concatenate Phenotypes objects
dim-Phenotypes-method: Dimension of a 'Phenotypes' object
gespeR-class: gespeR
join-methods: join
rbo: Rank biased overlap (Webber et al., 2010)
stabilityfits: Example fits for phenotypes from simulated screening data A,...
See all...

All man pages Function index File listing

Man pages

annotate.gsp-methods: annotate.gsp
as.data.frame.concordance: Coerce method
as.data.frame-Phenotypes-method: Convert Phenotypes object to a data.frame
concordance: Evaluate the concordance between Phenotype objects
c-Phenotypes-method: Concatenate Phenotypes objects
dim-Phenotypes-method: Dimension of a 'Phenotypes' object
gespeR-class: gespeR
gespeR-package: Package: Gene-Specific Phenotype EstimatoR
gspssp-methods: Retrieve GSPs and SSPs from 'gespeR' objects
join-methods: join
lasso.rand: Randomized Lasso
na.rem-methods: Remove NA/Inf values from phenotype vectors
path-methods: path
Phenotypes-class: Phenotypes
plot.concordance: Plot concordance
plot.gespeR: Plot method for 'gespeR' objects
plot.Phenotypes: Plot method for Phenotype objects
rbo: Rank biased overlap (Webber et al., 2010)
scores-methods: scores
simData: Example data: Simulated phenotypes and target relations for 4...
stabilityfits: Example fits for phenotypes from simulated screening data A,...
stability-methods: stability
stability.selection: Stability Selection
sub-Phenotypes-ANY-ANY-ANY-method: Subsetting for Phenotype objects.
sub-TargetRelations-ANY-ANY-ANY-method: Subsetting for TargetRelations objects.
TargetRelations-class: TargetRelations
target-relations-methods: target.relations
trmatrix-methods: Methods for values of 'TargetRelations' objects
values-methods: values

Functions

Phenotypes Man page
Phenotypes,Matrix-method Man page
Phenotypes,cellHTS-method Man page
Phenotypes,character-method Man page
Phenotypes-class Man page
TargetRelations Man page
TargetRelations,Matrix-method Man page
TargetRelations,character-method Man page
TargetRelations-class Man page
[,Phenotypes,ANY,ANY,ANY-method Man page
[,TargetRelations,ANY,ANY,ANY-method Man page
annotate.gsp Man page
annotate.gsp,Phenotypes-method Man page
annotate.gsp,gespeR-method Man page
as.data.frame,Phenotypes-method Man page
as.data.frame.concordance Man page Source code
bindphens Source code
c,Phenotypes-method Man page
concordance Man page Source code
dim,Phenotypes-method Man page
gespeR Man page
gespeR,Phenotypes,TargetRelations-method Man page
gespeR,numeric,Matrix-method Man page
gespeR-class Man page
gespeR-package Man page
gespeR.cv Source code
gespeR.stability Source code
gespeRpkg Man page
gsp Man page
gsp,gespeR-method Man page
jaccard Source code
join Man page
join,TargetRelations,Phenotypes-method Man page
lasso.rand Man page Source code
loadValues Man page
loadValues,TargetRelations-method Man page
loadValues,gespeR-method Man page
na.rem Man page
na.rem,Phenotypes-method Man page
path<- Man page
path<-,TargetRelations,character-method Man page
plot.Phenotypes Man page Source code
plot.concordance Man page Source code
plot.gespeR Man page Source code
rbo Man page Source code
rbo.ext Source code
scores Man page
scores,Phenotypes-method Man page
scores,gespeR-method Man page
select.ids Source code
select.model Source code
simData Man page
ssp Man page
ssp,gespeR-method Man page
stability Man page
stability,gespeR-method Man page
stability.selection Man page Source code
stabilityfits Man page
target.relations Man page
target.relations,gespeR-method Man page
unloadValues Man page
unloadValues,TargetRelations-method Man page
unloadValues,gespeR-method Man page
values Man page
values,Phenotypes-method Man page
values,TargetRelations-method Man page
writeValues Man page
writeValues,TargetRelations-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/Phenotypes-class.R
R/TargetRelations-class.R
R/gespeR-class.R
R/gespeR-concordance.R
R/gespeR-functions.R
R/gespeR-generics.R
R/gespeR-methods.R
R/gespeR-package.R
README.md
build
build/vignette.rds
data
data/stabilityfits.RData
inst
inst/doc
inst/doc/gespeR.R
inst/doc/gespeR.Rnw
inst/doc/gespeR.pdf
inst/example
inst/example/data_simulation.R
inst/example/gespeR-example.R
inst/extdata
inst/extdata/Phenotypes_screen_A.txt
inst/extdata/Phenotypes_screen_B.txt
inst/extdata/Phenotypes_screen_C.txt
inst/extdata/Phenotypes_screen_D.txt
inst/extdata/TR_screen_A.rds
inst/extdata/TR_screen_B.rds
inst/extdata/TR_screen_C.rds
inst/extdata/TR_screen_D.rds
man
man/Phenotypes-class.Rd
man/TargetRelations-class.Rd
man/annotate.gsp-methods.Rd
man/as.data.frame-Phenotypes-method.Rd
man/as.data.frame.concordance.Rd
man/c-Phenotypes-method.Rd
man/concordance.Rd
man/dim-Phenotypes-method.Rd
man/gespeR-class.Rd
man/gespeR-package.Rd
man/gspssp-methods.Rd
man/join-methods.Rd
man/lasso.rand.Rd
man/na.rem-methods.Rd
man/path-methods.Rd
man/plot.Phenotypes.Rd
man/plot.concordance.Rd
man/plot.gespeR.Rd
man/rbo.Rd
man/scores-methods.Rd
man/simData.Rd
man/stability-methods.Rd
man/stability.selection.Rd
man/stabilityfits.Rd
man/sub-Phenotypes-ANY-ANY-ANY-method.Rd
man/sub-TargetRelations-ANY-ANY-ANY-method.Rd
man/target-relations-methods.Rd
man/trmatrix-methods.Rd
man/values-methods.Rd
vignettes
vignettes/gespeR.Rnw
vignettes/tmp
vignettes/tmp/gespeR-plot_concordance-1.pdf
vignettes/tmp/gespeR-plot_concordance-2.pdf
vignettes/tmp/gespeR-plot_cv-1.pdf
vignettes/tmp/gespeR-plot_phenotypes-1.pdf
vignettes/workflow
vignettes/workflow/gespeR_GSPs.rds
vignettes/workflow/gespeR_deconvolute_screens.Rmd
vignettes/workflow/gespeR_deconvolute_screens.html
vignettes/workflow/gespeR_fits.rds
gespeR documentation built on May 20, 2017, 9:53 p.m.

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