bioassayR: Cross-target analysis of small molecule bioactivity
Version 1.14.0

bioassayR is a computational tool that enables simultaneous analysis of thousands of bioassay experiments performed over a diverse set of compounds and biological targets. Unique features include support for large-scale cross-target analyses of both public and custom bioassays, generation of high throughput screening fingerprints (HTSFPs), and an optional preloaded database that provides access to a substantial portion of publicly available bioactivity data.

AuthorTyler Backman, Ronly Schlenk, Thomas Girke
Bioconductor views Bioinformatics CellBasedAssays DataImport Infrastructure Metabolomics MicrotitrePlateAssay Proteomics Visualization
Date of publicationNone
MaintainerTyler Backman <tbackman@lbl.gov>
LicenseArtistic-2.0
Version1.14.0
URL https://github.com/TylerBackman/bioassayR
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("bioassayR")

Getting started

README.md
bioassayR Introduction and Examples

Popular man pages

addBioassayIndex: Index a bioassayR database
bioassay-class: Class '"bioassay"'
disconnectBioassayDB: Disconnect the database file from a 'BioassayDB' object
dropBioassay: Delete an assay from a bioassayR database
dropBioassayIndex: Remove index from a bioassayR database
getAssays: Retrieve multiple bioassays from a database
samplebioassay: Sample activity data for use with bioassayR
See all...

All man pages Function index File listing

Man pages

activeAgainst: Show compounds active against a specified target
activeTargets: Show targets against which a small molecule is active
addBioassayIndex: Index a bioassayR database
addDataSource: Add a new data source to a bioassayR database
allCids: List compound cids in a 'BioassayDB', 'bioassay',...
allTargets: List distinct target(s) in a 'BioassayDB', 'bioassay',...
assaySetTargets: Return targets of assays in a 'bioassaySet' object
bioactivityFingerprint: Create an 'ChemmineR' 'FPset' object that contains...
bioassay-class: Class '"bioassay"'
BioAssayDB-class: Class '"BioassayDB"'
bioassaySet-class: Class '"bioassaySet"'
connectBioassayDB: Create a 'BioassayDB' object connected to the specified...
crossReactivityProbability: Compute the probability that compounds in a compound vs...
disconnectBioassayDB: Disconnect the database file from a 'BioassayDB' object
dropBioassay: Delete an assay from a bioassayR database
dropBioassayIndex: Remove index from a bioassayR database
getAssay: Retrieve a bioassay
getAssays: Retrieve multiple bioassays from a database
getBioassaySetByCids: Create 'bioassaySet' sparse matrix object with activity data...
inactiveTargets: Takes a single cid and returns a table of the proteins it has...
loadBioassay: Add an assay to the database
loadIdMapping: Load a target identifier mapping into a bioassayR database
newBioassayDB: Create a new bioassayR database
parsePubChemBioassay: Parse PubChem Bioassay Data
perTargetMatrix: Collapse a 'bioassaySet' object from multiple assays by...
queryBioassayDB: Perform a SQL query on a bioassayR database
samplebioassay: Sample activity data for use with bioassayR
scaleBioassaySet: Centers and standardizes the numeric activity scores for a...
screenedAtLeast: Return all compounds in the database screened at least...
selectiveAgainst: Identify small molecules with selective binding against a...
targetSelectivity: Returns the target selectivity for a specified list of...
translateTargetId: Translate a protein target identifier to another identifier...
trinarySimilarity: Computes the tanimoto similarity coefficient between the...

Functions

BioassayDB-class Man page
activeAgainst Man page Source code
activeTargets Man page Source code
activity Man page
activity,bioassaySet-method Man page
activity<- Man page
activity<-,bioassaySet-method Man page
activityByAids Source code
activityByCids Source code
addAssayTarget Source code
addBioassayIndex Man page Source code
addDataSource Man page Source code
aid Man page
aid,bioassay-method Man page
aid<- Man page
aid<-,bioassay-method Man page
allCategories Source code
allCids Man page Source code Source code
allTargets Man page Source code Source code
assaySetTargets Man page Source code
assay_type Man page
assay_type,bioassay-method Man page
assay_type,bioassaySet-method Man page
assay_type<- Man page
assay_type<-,bioassay-method Man page
assay_type<-,bioassaySet-method Man page
assaysByAids Source code
bioactivityFingerprint Man page Source code
bioassay Man page
bioassay-class Man page
bioassaySet-class Man page
cidsByTarget Source code
connectBioassayDB Man page Source code
crossReactivityPrior Man page Source code
crossReactivityProbability Man page Source code
disconnectBioassayDB Man page Source code
dropBioassay Man page Source code
dropBioassayIndex Man page Source code
getAssay Man page Source code
getAssays Man page Source code
getBioassaySetByCids Man page Source code
inactiveTargets Man page Source code
loadBioassay Man page Source code
loadIdMapping Man page Source code
loadScores Source code
newBioassayDB Man page Source code
organism Man page
organism,bioassay-method Man page
organism,bioassaySet-method Man page
organism<- Man page
organism<-,bioassay-method Man page
organism<-,bioassaySet-method Man page
parsePubChemBioassay Man page Source code
perTargetMatrix Man page Source code
queryBioassayDB Man page
queryBioassayDB,BioassayDB-method Man page
reverseTranslateTargetId Source code
samplebioassay Man page
scaleBioassaySet Man page Source code
scores Man page
scores,bioassay-method Man page
scores,bioassaySet-method Man page
scores<- Man page
scores<-,bioassay-method Man page
scores<-,bioassaySet-method Man page
scoring Man page
scoring,bioassay-method Man page
scoring,bioassaySet-method Man page
scoring<- Man page
scoring<-,bioassay-method Man page
scoring<-,bioassaySet-method Man page
screenedAtLeast Man page Source code Source code
selectiveAgainst Man page Source code
show Man page
show,BioassayDB-method Man page
show,bioassay-method Man page
show,bioassaySet-method Man page
source_id Man page
source_id,bioassay-method Man page
source_id,bioassaySet-method Man page
source_id<- Man page
source_id<-,bioassay-method Man page
source_id<-,bioassaySet-method Man page
sources Man page
sources,bioassaySet-method Man page
sources<- Man page
sources<-,bioassaySet-method Man page
sourcesByAids Source code
targetSelectivity Man page Source code
target_types Man page
target_types,bioassay-method Man page
target_types,bioassaySet-method Man page
target_types<- Man page
target_types<-,bioassay-method Man page
target_types<-,bioassaySet-method Man page
targets Man page
targets,bioassay-method Man page
targets,bioassaySet-method Man page
targets<- Man page
targets<-,bioassay-method Man page
targets<-,bioassaySet-method Man page
targetsByAids Source code
targetsByCid Source code
translateTargetId Man page Source code Source code
trinarySimilarity Man page Source code
writeable Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/BioassayDB-accessors.R
R/bayesian-cross-reactivity.R
R/bioassay-accessors.R
R/bioassaySet-accessors.R
R/loadingData.R
R/queries.R
R/similarity.R
README.md
build
build/vignette.rds
data
data/samplebioassay.rda
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/bioassayR.R
inst/doc/bioassayR.Rmd
inst/doc/bioassayR.html
inst/extdata
inst/extdata/exampleAssay.xml
inst/extdata/exampleScores.csv
inst/extdata/sampleDatabase.sqlite
man
man/BioAssayDB-class.Rd
man/activeAgainst.Rd
man/activeTargets.Rd
man/addBioassayIndex.Rd
man/addDataSource.Rd
man/allCids.Rd
man/allTargets.Rd
man/assaySetTargets.Rd
man/bioactivityFingerprint.Rd
man/bioassay-class.Rd
man/bioassaySet-class.Rd
man/connectBioassayDB.Rd
man/crossReactivityProbability.Rd
man/disconnectBioassayDB.Rd
man/dropBioassay.Rd
man/dropBioassayIndex.Rd
man/getAssay.Rd
man/getAssays.Rd
man/getBioassaySetByCids.Rd
man/inactiveTargets.Rd
man/loadBioassay.Rd
man/loadIdMapping.Rd
man/newBioassayDB.Rd
man/parsePubChemBioassay.Rd
man/perTargetMatrix.Rd
man/queryBioassayDB.Rd
man/samplebioassay.Rd
man/scaleBioassaySet.Rd
man/screenedAtLeast.Rd
man/selectiveAgainst.Rd
man/targetSelectivity.Rd
man/translateTargetId.Rd
man/trinarySimilarity.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test_bioactivityFingerprint.R
tests/testthat/test_crossReactivityProbability.R
tests/testthat/test_perTargetMatrix.R
tests/testthat/test_scaleBioassaySet.R
tests/testthat/test_targetSelectivity.R
tests/testthat/test_trinarySimilarity.R
vignettes
vignettes/Makefile
vignettes/Makefile_bootstrap
vignettes/bibtex.bib
vignettes/bioassayR.Rmd
vignettes/bioassayR_cache
vignettes/bioassayR_cache/html
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bioassayR documentation built on May 20, 2017, 9:34 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

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