bioassayR: Cross-target analysis of small molecule bioactivity

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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.

Author
Tyler Backman, Ronly Schlenk, Thomas Girke
Date of publication
None
Maintainer
Tyler Backman <tbackman@lbl.gov>
License
Artistic-2.0
Version
1.12.1
URLs

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