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.

Author
Fabian Schmich
Date of publication
None
Maintainer
Fabian Schmich <fabian.schmich@bsse.ethz.ch>
License
GPL-3
Version
1.6.0
URLs

View on Bioconductor

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

Files in this package

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