Package: gespeR 1.37.0

Fabian Schmich

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.

Authors:Fabian Schmich

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gespeR.pdf |gespeR.html✨
gespeR/json (API)

# Install 'gespeR' in R:

install.packages('gespeR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

The latest version of this package failed to build. Look at thebuild logs for more information.

Datasets:

stabilityfits - Example fits for phenotypes from simulated screening data A, B, C and D

On BioConductor:gespeR-1.35.0(bioc 3.19)gespeR-1.34.0(bioc 3.18)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

21 exports 0.91 score 110 dependencies 4 mentions

Last updated 2 months agofrom:44a1e66635

Exports:annotate.gsp as.data.frame concordance gespeR gsp join lasso.rand loadValues na.rem path<-Phenotypes rbo scores ssp stability stability.selection target.relations TargetRelations unloadValues values writeValues

Dependencies:affy affyio annotate AnnotationDbi askpass BH Biobase BiocFileCache BiocGenerics BiocManager biomaRt Biostrings bit bit64 blob cachem Category cellHTS2 cli codetools colorspace cpp11 crayon curl DBI dbplyr digest doParallel dplyr fansi farver fastmap filelock foreach genefilter generics GenomeInfoDb GenomeInfoDbData ggplot2 glmnet glue graph GSEABase gtable hms httr httr2 hwriter IRanges isoband iterators jsonlite KEGGREST labeling lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr plyr png preprocessCore prettyunits progress purrr R6 rappdirs RBGL RColorBrewer Rcpp RcppEigen reshape2 rlang RSQLite S4Vectors scales shape splots statmod stringi stringr survival sys tibble tidyr tidyselect UCSC.utils utf8 vctrs viridisLite vsn withr XML xml2 xtable XVector zlibbioc

An R package for deconvoluting off-target confounded RNAi screens

Rendered fromgespeR.Rnwusingknitr::knitron May 01 2024.

Last update: 2015-08-03
Started: 2014-12-13

Development and contributors

Readme and manuals

Help Manual

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