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.

AuthorTyler Backman, Ronly Schlenk, Thomas Girke
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...

Files in this package

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

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

All documentation is copyright its authors; we didn't write any of that.