Package: bioassayR 1.51.0

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

bioassayR_1.51.0.tar.gz
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bioassayR_1.51.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
bioassayR/json (API)

# Install 'bioassayR' in R:

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

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

Datasets:

samplebioassay - Sample activity data for use with bioassayR

On BioConductor:bioassayR-1.51.0(bioc 3.24)bioassayR-1.50.0(bioc 3.23)

immunooncology microtitreplateassay cellbasedassays visualization infrastructure dataimport bioinformatics proteomics metabolomics

6.49 score 6 stars 47 scripts 1 mentions 51 exports 67 dependencies

Last updated from:e819fa680d. Checks:3 ERROR, 5 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	190
linux-devel-x86_64	NOTE	273
source / vignettes	OK	244
linux-release-x86_64	NOTE	249
macos-release-arm64	ERROR	135
macos-oldrel-arm64	ERROR	140
windows-devel	NOTE	169
windows-release	NOTE	148
windows-oldrel	NOTE	145
wasm-release	OK	194

Exports:activeAgainst activeTargets activity activity<-addBioassayIndex addDataSource aid aid<-allCids allTargets assay_type assay_type<-assaySetTargets bioactivityFingerprint connectBioassayDB crossReactivityPrior crossReactivityProbability disconnectBioassayDB dropBioassay dropBioassayIndex getAssay getAssays getBioassaySetByCids inactiveTargets loadBioassay loadIdMapping newBioassayDB organism organism<-parsePubChemBioassay perTargetMatrix queryBioassayDB scaleBioassaySet scores scores<-scoring scoring<-screenedAtLeast selectiveAgainst show source_id source_id<-sources sources<-target_types target_types<-targets targets<-targetSelectivity translateTargetId trinarySimilarity

Dependencies:base64enc BH BiocGenerics bit bit64 bitops blob bslib cachem ChemmineR cli cpp11 crosstalk DBI digest DT evaluate farver fastmap fontawesome fs generics ggplot2 glue gridExtra gtable highr htmltools htmlwidgets isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle magrittr Matrix memoise mime otel pkgconfig png promises R6 rappdirs RColorBrewer Rcpp RCurl rjson rlang rmarkdown RSQLite rsvg S7 sass scales stringi tinytex vctrs viridisLite withr xfun XML yaml

bioassayR Introduction and Examples

Rendered frombioassayR.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Show compounds active against a specified target	activeAgainst
Show targets against which a small molecule is active	activeTargets
Index a bioassayR database	addBioassayIndex
Add a new data source to a bioassayR database	addDataSource
List compound cids in a 'BioassayDB', 'bioassay', 'bioassaySet', or target matrix ('dgCMatrix') object	allCids
List distinct target(s) in a 'BioassayDB', 'bioassay', 'bioassaySet', or target matrix ('dgCMatrix') object	allTargets
Return targets of assays in a 'bioassaySet' object	assaySetTargets
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 file	connectBioassayDB
Compute the probability that compounds in a compound vs target matrix are promiscuous binders	crossReactivityPrior crossReactivityProbability
Disconnect the database file from a 'BioassayDB' object	disconnectBioassayDB
Delete an assay from a bioassayR database	dropBioassay
Remove index from a bioassayR database	dropBioassayIndex
Retrieve a bioassay	getAssay
Retrieve multiple bioassays from a database	getAssays
Create 'bioassaySet' sparse matrix object with activity data only for specified compounds	getBioassaySetByCids
Takes a single cid and returns a table of the proteins it has been found inactive against.	inactiveTargets
Add an assay to the database	loadBioassay
Load a target identifier mapping into a bioassayR database	loadIdMapping
Create a new bioassayR database	newBioassayDB
Parse PubChem Bioassay Data	parsePubChemBioassay
Collapse a 'bioassaySet' object from multiple assays by combining assays with a common target	perTargetMatrix
Perform a SQL query on a bioassayR database	queryBioassayDB
Sample activity data for use with bioassayR	samplebioassay
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 interest	selectiveAgainst
Returns the target selectivity for a specified list of compounds (cids).	targetSelectivity
Translate a protein target identifier to another identifier system	translateTargetId
Computes the tanimoto similarity coefficient between the bioactivity profiles of two compounds, each represented as a column in a compound vs. target sparse matrix	trinarySimilarity