gespeR: Gene-Specific Phenotype EstimatoR

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
Date of publicationNone
MaintainerFabian Schmich <fabian.schmich@bsse.ethz.ch>
LicenseGPL-3
Version1.6.0
http://www.cbg.ethz.ch/software/gespeR

View on Bioconductor

Functions

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

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

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.