Package: Xeva 1.28.0

Benjamin Haibe-Kains

Xeva: Analysis of patient-derived xenograft (PDX) data

The Xeva package provides efficient and powerful functions for patient-drived xenograft (PDX) based pharmacogenomic data analysis. This package contains a set of functions to perform analysis of patient-derived xenograft data. This package was developed by the BHKLab, for further information please see our documentation.

Authors:Arvind Mer [aut], Benjamin Haibe-Kains [aut, cre]

Xeva_1.28.0.tar.gz
Xeva_1.28.0.zip(r-4.7-any)Xeva_1.28.0.zip(r-4.6-any)Xeva_1.28.0.zip(r-4.5-any)
Xeva_1.28.0.tgz(r-4.6-any)Xeva_1.28.0.tgz(r-4.5-any)
Xeva_1.28.0.tar.gz(r-4.7-any)Xeva_1.28.0.tar.gz(r-4.6-any)
Xeva_1.28.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Xeva/json (API)

# Install 'Xeva' in R:

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

Bug tracker:https://github.com/bhklab/xeva/issues

Datasets:

brca - PDXE breast cancer dataset
PDXMI - PDX-MI data
repdx - Example PDX dataset

On BioConductor:Xeva-1.29.0(bioc 3.24)Xeva-1.28.0(bioc 3.23)

geneexpression pharmacogenetics pharmacogenomics software classification

6.75 score 11 stars 51 scripts 484 downloads 28 exports 150 dependencies

Last updated from:a30472f7a1 (on RELEASE_3_23). Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: no.
A new build is currently in progress.

Target	Result	Time
bioc-checks	WARNING	231
linux-devel	NOTE	453
source / vignettes	OK	426
linux-release	NOTE	451
macos-release	NOTE	282
macos-oldrel	NOTE	270
windows-devel	NOTE	256
windows-release	NOTE	315
windows-oldrel	NOTE	227
wasm-release	OK	174

Exports:ABC addExperimentalDesign angle AUC batchInfo createXevaSet dosePlot downloadXevaSet drugInform drugSensitivitySig getExperiment getMolecularProfiles lmm modelInfo mRECIST plotBatch plotmRECIST plotPDX response selectModelIds sensitivity setResponse slope subsetXeva summarizeMolecularProfiles summarizeResponse TGI waterfall

Dependencies:abind backports base64enc BBmisc bench BH Biobase BiocBaseUtils BiocGenerics BiocParallel bitops boot bslib BumpyMatrix cachem caTools celestial checkmate circlize cli clue cluster codetools colorspace commonmark ComplexHeatmap coop CoreGx cowplot cpp11 crayon crosstalk data.table DelayedArray digest doParallel downloader dplyr DT evaluate farver fastmap fastmatch fgsea fontawesome foreach formatR fs futile.logger futile.options generics GenomicRanges GetoptLong ggplot2 GlobalOptions glue gplots gtable gtools highr htmltools htmlwidgets httpuv igraph IRanges isoband iterators jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle limma lsa magicaxis magrittr mapproj maps marray MASS Matrix MatrixGenerics matrixStats memoise mime MultiAssayExperiment NISTunits nlme otel PharmacoGx piano pillar pkgconfig plotrix plyr png pracma profmem promises purrr R6 RANN rappdirs RColorBrewer Rcpp relations reshape2 rjson rlang rmarkdown Rmisc S4Arrays S4Vectors S7 sass scales Seqinfo sets shape shiny shinydashboard shinyjs slam sm snow SnowballC sourcetools SparseArray statmod stringi stringr SummarizedExperiment tibble tidyr tidyselect tinytex utf8 vctrs viridisLite visNetwork withr xfun xtable XVector yaml

The Xeva User's Guide

Rendered fromXeva.Rnwusingknitr::knitr

Last update: 2023-04-19
Started: 2019-03-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
area between curves Computes the area between two time-volume curves.	ABC
Add a new experimental design	addExperimentalDesign addExperimentalDesign,XevaSet-method
compute angle Computes the angle between two time-volume curves.	angle
area under the curve 'AUC' Returns area under the curve	AUC
Get batch information	batchInfo batchInfo,XevaSet-method
PDXE breast cancer dataset	brca
XevaSet constructor	createXevaSet
plot dose data	dosePlot
Download a XevaSet object or table of available XevaSet objects	downloadXevaSet
Get drug information Get the drug information slot from a XevaSet object.	drugInform drugInform,XevaSet-method
get drug sensitivity values	drugSensitivitySig
Get PDX experiment data	getExperiment getExperiment,XevaSet-method
Get molecular profiles from a XevaSet object	getMolecularProfiles
linear mixed model	lmm
modelInfo Generic Generic for modelInfo method	modelInfo modelInfo,XevaSet-method
Computes the mRECIST	mRECIST
PDX-MI data	PDXMI
To plot mRECIST values	plotmRECIST
Plot batch data	plotBatch plotPDX
Print the batch response	print.batchResponse
Print the model response	print.modelResponse
Print the pdx batch	print.pdxBatch
Example PDX dataset	repdx
compute PDX response	response
To select model IDs based on drug name and/or tissue type.	selectModelIds selectModelIds,XevaSet-method
Get sensitivity for an Xeva object	sensitivity
set PDX response	setResponse
Computes slope	slope
Subset Xeva object.	subsetXeva
Summarize molecular profiles	summarizeMolecularProfiles
Summarize Response of PDXs	summarizeResponse
tumor growth inhibition (TGI) Computes the tumor growth inhibition (TGI) between two time-volume curves	TGI
waterfall plot Creates waterfall plot for a given drug.	waterfall