bioassayR: Cross-target analysis of small molecule bioactivity

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("bioassayR")
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
Version1.12.1
https://github.com/TylerBackman/bioassayR

View on Bioconductor

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

activeAgainst Man page
activeTargets Man page
activity Man page
activity<- Man page
activity<-,bioassaySet-method Man page
activity,bioassaySet-method Man page
addBioassayIndex Man page
addDataSource Man page
aid Man page
aid<- Man page
aid<-,bioassay-method Man page
aid,bioassay-method Man page
allCids Man page
allTargets Man page
assaySetTargets Man page
assay_type Man page
assay_type<- Man page
assay_type<-,bioassay-method Man page
assay_type,bioassay-method Man page
assay_type<-,bioassaySet-method Man page
assay_type,bioassaySet-method Man page
bioactivityFingerprint Man page
bioassay Man page
bioassay-class Man page
BioassayDB-class Man page
bioassaySet-class Man page
connectBioassayDB Man page
crossReactivityPrior Man page
crossReactivityProbability Man page
disconnectBioassayDB Man page
dropBioassay Man page
dropBioassayIndex Man page
getAssay Man page
getAssays Man page
getBioassaySetByCids Man page
inactiveTargets Man page
loadBioassay Man page
loadIdMapping Man page
newBioassayDB Man page
organism Man page
organism<- Man page
organism<-,bioassay-method Man page
organism,bioassay-method Man page
organism<-,bioassaySet-method Man page
organism,bioassaySet-method Man page
parsePubChemBioassay Man page
perTargetMatrix Man page
queryBioassayDB Man page
queryBioassayDB,BioassayDB-method Man page
samplebioassay Man page
scaleBioassaySet Man page
scores Man page
scores<- Man page
scores<-,bioassay-method Man page
scores,bioassay-method Man page
scores<-,bioassaySet-method Man page
scores,bioassaySet-method Man page
scoring Man page
scoring<- Man page
scoring<-,bioassay-method Man page
scoring,bioassay-method Man page
scoring<-,bioassaySet-method Man page
scoring,bioassaySet-method Man page
screenedAtLeast Man page
selectiveAgainst Man page
show Man page
show,BioassayDB-method Man page
show,bioassay-method Man page
show,bioassaySet-method Man page
source_id Man page
source_id<- Man page
source_id<-,bioassay-method Man page
source_id,bioassay-method Man page
source_id<-,bioassaySet-method Man page
source_id,bioassaySet-method Man page
sources Man page
sources<- Man page
sources<-,bioassaySet-method Man page
sources,bioassaySet-method Man page
targets Man page
targets<- Man page
targets<-,bioassay-method Man page
targets,bioassay-method Man page
targets<-,bioassaySet-method Man page
targets,bioassaySet-method Man page
targetSelectivity Man page
target_types Man page
target_types<- Man page
target_types<-,bioassay-method Man page
target_types,bioassay-method Man page
target_types<-,bioassaySet-method Man page
target_types,bioassaySet-method Man page
translateTargetId Man page
trinarySimilarity Man page

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/bibtex.bib
vignettes/bioassayR.Rmd
vignettes/figures
vignettes/figures/bioassayR.png
vignettes/figures/bioassayR.svg
vignettes/getBM.RData
vignettes/getids.RData

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