Package: bioassayR 1.45.0

Thomas Girke

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.

Authors:Tyler Backman, Ronly Schlenk, Thomas Girke

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bioassayR.pdf |bioassayR.html✨
bioassayR/json (API)
NEWS

# Install 'bioassayR' in R:
install.packages('bioassayR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/girke-lab/bioassayr/issues

Datasets:

On BioConductor:bioassayR-1.45.0(bioc 3.21)bioassayR-1.44.0(bioc 3.20)

immunooncologymicrotitreplateassaycellbasedassaysvisualizationinfrastructuredataimportbioinformaticsproteomicsmetabolomics

6.70 score 5 stars 46 scripts 348 downloads 1 mentions 51 exports 76 dependencies

Last updated 2 months agofrom:248466e900. Checks:OK: 2 NOTE: 3 ERROR: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 18 2024
R-4.5-winNOTEDec 18 2024
R-4.5-linuxNOTEDec 18 2024
R-4.4-winNOTEDec 18 2024
R-4.4-macERRORDec 18 2024
R-4.3-winOKDec 18 2024
R-4.3-macERRORDec 18 2024

Exports:activeAgainstactiveTargetsactivityactivity<-addBioassayIndexaddDataSourceaidaid<-allCidsallTargetsassay_typeassay_type<-assaySetTargetsbioactivityFingerprintconnectBioassayDBcrossReactivityPriorcrossReactivityProbabilitydisconnectBioassayDBdropBioassaydropBioassayIndexgetAssaygetAssaysgetBioassaySetByCidsinactiveTargetsloadBioassayloadIdMappingnewBioassayDBorganismorganism<-parsePubChemBioassayperTargetMatrixqueryBioassayDBscaleBioassaySetscoresscores<-scoringscoring<-screenedAtLeastselectiveAgainstshowsource_idsource_id<-sourcessources<-target_typestarget_types<-targetstargets<-targetSelectivitytranslateTargetIdtrinarySimilarity

Dependencies:base64encBHBiocGenericsbitbit64bitopsblobbslibcachemChemmineRclicolorspacecpp11crosstalkDBIdigestDTevaluatefansifarverfastmapfontawesomefsgenericsggplot2gluegridExtragtablehighrhtmltoolshtmlwidgetshttpuvisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmepillarpkgconfigplogrpngpromisesR6rappdirsRColorBrewerRcppRCurlrjsonrlangrmarkdownRSQLitersvgsassscalesstringitibbletinytexutf8vctrsviridisLitewithrxfunXMLyaml

bioassayR Introduction and Examples

Authors: Tyler Backman, Thomas Girke

Rendered frombioassayR.Rmdusingknitr::rmarkdownon Dec 18 2024.

Last update: 2024-10-22
Started: 2015-10-07

Readme and manuals

Help Manual

Help pageTopics
Show compounds active against a specified targetactiveAgainst
Show targets against which a small molecule is activeactiveTargets
Index a bioassayR databaseaddBioassayIndex
Add a new data source to a bioassayR databaseaddDataSource
List compound cids in a 'BioassayDB', 'bioassay', 'bioassaySet', or target matrix ('dgCMatrix') objectallCids
List distinct target(s) in a 'BioassayDB', 'bioassay', 'bioassaySet', or target matrix ('dgCMatrix') objectallTargets
Return targets of assays in a 'bioassaySet' objectassaySetTargets
Create an 'ChemmineR' 'FPset' object that contains bioactivity results for a given set of compounds and targets.bioactivityFingerprint
Class '"bioassay"'aid aid,bioassay-method aid<- aid<-,bioassay-method assay_type assay_type,bioassay-method assay_type<- assay_type<-,bioassay-method bioassay bioassay-class organism organism,bioassay-method organism<- organism<-,bioassay-method scores scores,bioassay-method scores<- scores<-,bioassay-method scoring scoring,bioassay-method scoring<- scoring<-,bioassay-method show show,bioassay-method source_id source_id,bioassay-method source_id<- source_id<-,bioassay-method targets targets,bioassay-method targets<- targets<-,bioassay-method target_types target_types,bioassay-method target_types<- target_types<-,bioassay-method
Class '"BioassayDB"'BioassayDB-class queryBioassayDB,BioassayDB-method show,BioassayDB-method
Class '"bioassaySet"'activity activity,bioassaySet-method activity<- activity<-,bioassaySet-method assay_type,bioassaySet-method assay_type<-,bioassaySet-method bioassaySet-class organism,bioassaySet-method organism<-,bioassaySet-method scores,bioassaySet-method scores<-,bioassaySet-method scoring,bioassaySet-method scoring<-,bioassaySet-method show,bioassaySet-method sources sources,bioassaySet-method sources<- sources<-,bioassaySet-method source_id,bioassaySet-method source_id<-,bioassaySet-method targets,bioassaySet-method targets<-,bioassaySet-method target_types,bioassaySet-method target_types<-,bioassaySet-method
Create a 'BioassayDB' object connected to the specified database fileconnectBioassayDB
Compute the probability that compounds in a compound vs target matrix are promiscuous binderscrossReactivityPrior crossReactivityProbability
Disconnect the database file from a 'BioassayDB' objectdisconnectBioassayDB
Delete an assay from a bioassayR databasedropBioassay
Remove index from a bioassayR databasedropBioassayIndex
Retrieve a bioassaygetAssay
Retrieve multiple bioassays from a databasegetAssays
Create 'bioassaySet' sparse matrix object with activity data only for specified compoundsgetBioassaySetByCids
Takes a single cid and returns a table of the proteins it has been found inactive against.inactiveTargets
Add an assay to the databaseloadBioassay
Load a target identifier mapping into a bioassayR databaseloadIdMapping
Create a new bioassayR databasenewBioassayDB
Parse PubChem Bioassay DataparsePubChemBioassay
Collapse a 'bioassaySet' object from multiple assays by combining assays with a common targetperTargetMatrix
Perform a SQL query on a bioassayR databasequeryBioassayDB
Sample activity data for use with bioassayRsamplebioassay
Centers and standardizes the numeric activity scores for a 'bioassaySet' object (creates Z-scores)scaleBioassaySet
Return all compounds in the database screened at least 'minTargets' times.screenedAtLeast
Identify small molecules with selective binding against a target of interestselectiveAgainst
Returns the target selectivity for a specified list of compounds (cids).targetSelectivity
Translate a protein target identifier to another identifier systemtranslateTargetId
Computes the tanimoto similarity coefficient between the bioactivity profiles of two compounds, each represented as a column in a compound vs. target sparse matrixtrinarySimilarity