{ "_id": "6a2514a44b233be19838b02f", "Package": "bioassayR", "Type": "Package", "Title": "Cross-target analysis of small molecule bioactivity", "Version": "1.50.0", "Date": "2024-10-21", "Author": "Tyler Backman, Ronly Schlenk, Thomas Girke", "Maintainer": "Thomas Girke ", "Description": "bioassayR is a computational tool that enables\nsimultaneous analysis of thousands of bioassay experiments\nperformed over a diverse set of compounds and biological\ntargets. Unique features include support for large-scale\ncross-target analyses of both public and custom bioassays,\ngeneration of high throughput screening fingerprints (HTSFPs),\nand an optional preloaded database that provides access to a\nsubstantial portion of publicly available bioactivity data.", "URL": "https://github.com/girke-lab/bioassayR", "BugReports": "https://github.com/girke-lab/bioassayR/issues", "License": "Artistic-2.0", "biocViews": "ImmunoOncology, MicrotitrePlateAssay, CellBasedAssays,\nVisualization, Infrastructure, DataImport, Bioinformatics,\nProteomics, Metabolomics", "LazyLoad": "yes", "Collate": "AllClasses.R AllGenerics.R BioassayDB-accessors.R\nbioassay-accessors.R loadingData.R queries.R\nbioassaySet-accessors.R bayesian-cross-reactivity.R\nsimilarity.R", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev librsvg2-dev\nlibuv1-dev libxml2-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:38:14 UTC", "RemoteUrl": "https://github.com/bioc/bioassayR", "RemoteRef": "RELEASE_3_23", "RemoteSha": "b239b42ff4e20992903b7c6fce7c665494386281", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-07 06:45:24 UTC", "User": "root" }, "MD5sum": "581e79f9463039b98a7c2dc6404106e5", "_user": "bioc-release", "_type": "src", "_file": "bioassayR_1.50.0.tar.gz", "_fileid": "1e2aeabf6380706c2a34d8feeb1891604af851839169daa40e1f10bf2362f1db", "_filesize": 1837424, "_sha256": "1e2aeabf6380706c2a34d8feeb1891604af851839169daa40e1f10bf2362f1db", "_created": "2026-06-07T06:45:24.000Z", "_published": "2026-06-07T06:50:11.954Z", "_jobs": [ { "job": 79938456672, "time": 165, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7461596342" }, { "job": 79938456686, "time": 244, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7461605187" }, { "job": 79938456678, "time": 235, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7461604302" }, { "job": 79938456695, "time": 151, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7461594647" }, { "job": 79938456680, "time": 179, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7461597910" }, { "job": 79938193672, "time": 248, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7461577155" }, { "job": 79938456676, "time": 162, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7461595892" }, { "job": 79938456685, "time": 161, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7461595743" }, { "job": 79938456688, "time": 144, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7461593868" }, { "job": 79938456679, "time": 165, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7461596375" } ], "_bioccheck": { "error": 1, "warning": 5, "note": 11 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27085191108", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/bioassayR", "_commit": { "id": "b239b42ff4e20992903b7c6fce7c665494386281", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777379894 }, "_maintainer": { "name": "Thomas Girke", "email": "tgirke@citrus.ucr.edu", "login": "tgirke", "description": "", "uuid": 1336916 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "DBI", "version": ">= 0.3.1", "role": "Depends" }, { "package": "RSQLite", "version": ">= 1.0.0", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "Matrix", "role": "Depends" }, { "package": "rjson", "role": "Depends" }, { "package": "BiocGenerics", "version": ">= 0.13.8", "role": "Depends" }, { "package": "XML", "role": "Imports" }, { "package": "ChemmineR", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "RCurl", "role": "Suggests" }, { "package": "biomaRt", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "knitcitations", "role": "Suggests" }, { "package": "knitrBootstrap", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.51.0", "bioc": "3.24" }, { "branch": "release", "version": "1.50.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "microtitreplateassay", "cellbasedassays", "visualization", "infrastructure", "dataimport", "bioinformatics", "proteomics", "metabolomics" ], "_stars": 6, "_contributors": [ { "user": "dtenenba", "count": 16, "uuid": 2286826 }, { "user": "tylerbackman", "count": 16, "uuid": 647482 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "dcassol", "count": 12, "uuid": 12722576 }, { "user": "jwokaty", "count": 8, "uuid": 1744257 }, { "user": "tgirke", "count": 4, "uuid": 1336916 }, { "user": "hpages", "count": 2, "uuid": 8810451 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "kayla-morrell", "count": 1, "uuid": 32339524 }, { "user": "link-ny", "count": 1, "uuid": 4392950 }, { "user": "mtmorgan", "count": 1, "uuid": 118552 }, { "user": "sonali-bioc", "count": 1, "uuid": 6373953 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 470, "source": "https://www.bioconductor.org/packages/stats/bioc/bioassayR" }, "_devurl": "https://github.com/girke-lab/bioassayr", "_searchresults": 47, "_rbuild": "4.6.0", "_assets": [ "extra/bioassayR.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/girke-lab/bioassayr", "_realowner": "bioc", "_cranurl": false, "_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" ], "_datasets": [ { "name": "samplebioassay", "title": "Sample activity data for use with bioassayR", "object": "samplebioassay", "file": "samplebioassay.rda", "class": [ "data.frame" ], "fields": [ "cid", "activity", "score" ], "rows": 57, "table": true, "tojson": true } ], "_help": [ { "page": "activeAgainst", "title": "Show compounds active against a specified target", "topics": [ "activeAgainst" ] }, { "page": "activeTargets", "title": "Show targets against which a small molecule is active", "topics": [ "activeTargets" ] }, { "page": "addBioassayIndex", "title": "Index a bioassayR database", "topics": [ "addBioassayIndex" ] }, { "page": "addDataSource", "title": "Add a new data source to a bioassayR database", "topics": [ "addDataSource" ] }, { "page": "allCids", "title": "List compound cids in a 'BioassayDB', 'bioassay', 'bioassaySet', or target matrix ('dgCMatrix') object", "topics": [ "allCids" ] }, { "page": "allTargets", "title": "List distinct target(s) in a 'BioassayDB', 'bioassay', 'bioassaySet', or target matrix ('dgCMatrix') object", "topics": [ "allTargets" ] }, { "page": "assaySetTargets", "title": "Return targets of assays in a 'bioassaySet' object", "topics": [ "assaySetTargets" ] }, { "page": "bioactivityFingerprint", "title": "Create an 'ChemmineR' 'FPset' object that contains bioactivity results for a given set of compounds and targets.", "topics": [ "bioactivityFingerprint" ] }, { "page": "bioassay-class", "title": "Class '\"bioassay\"'", "topics": [ "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" ] }, { "page": "BioAssayDB-class", "title": "Class '\"BioassayDB\"'", "topics": [ "BioassayDB-class", "queryBioassayDB,BioassayDB-method", "show,BioassayDB-method" ] }, { "page": "bioassaySet-class", "title": "Class '\"bioassaySet\"'", "topics": [ "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" ] }, { "page": "connectBioassayDB", "title": "Create a 'BioassayDB' object connected to the specified database file", "topics": [ "connectBioassayDB" ] }, { "page": "crossReactivityProbability", "title": "Compute the probability that compounds in a compound vs target matrix are promiscuous binders", "topics": [ "crossReactivityPrior", "crossReactivityProbability" ] }, { "page": "disconnectBioassayDB", "title": "Disconnect the database file from a 'BioassayDB' object", "topics": [ "disconnectBioassayDB" ] }, { "page": "dropBioassay", "title": "Delete an assay from a bioassayR database", "topics": [ "dropBioassay" ] }, { "page": "dropBioassayIndex", "title": "Remove index from a bioassayR database", "topics": [ "dropBioassayIndex" ] }, { "page": "getAssay", "title": "Retrieve a bioassay", "topics": [ "getAssay" ] }, { "page": "getAssays", "title": "Retrieve multiple bioassays from a database", "topics": [ "getAssays" ] }, { "page": "getBioassaySetByCids", "title": "Create 'bioassaySet' sparse matrix object with activity data only for specified compounds", "topics": [ "getBioassaySetByCids" ] }, { "page": "inactiveTargets", "title": "Takes a single cid and returns a table of the proteins it has been found inactive against.", "topics": [ "inactiveTargets" ] }, { "page": "loadBioassay", "title": "Add an assay to the database", "topics": [ "loadBioassay" ] }, { "page": "loadIdMapping", "title": "Load a target identifier mapping into a bioassayR database", "topics": [ "loadIdMapping" ] }, { "page": "newBioassayDB", "title": "Create a new bioassayR database", "topics": [ "newBioassayDB" ] }, { "page": "parsePubChemBioassay", "title": "Parse PubChem Bioassay Data", "topics": [ "parsePubChemBioassay" ] }, { "page": "perTargetMatrix", "title": "Collapse a 'bioassaySet' object from multiple assays by combining assays with a common target", "topics": [ "perTargetMatrix" ] }, { "page": "queryBioassayDB", "title": "Perform a SQL query on a bioassayR database", "topics": [ "queryBioassayDB" ] }, { "page": "samplebioassay", "title": "Sample activity data for use with bioassayR", "topics": [ "samplebioassay" ] }, { "page": "scaleBioassaySet", "title": "Centers and standardizes the numeric activity scores for a 'bioassaySet' object (creates Z-scores)", "topics": [ "scaleBioassaySet" ] }, { "page": "screenedAtLeast", "title": "Return all compounds in the database screened at least 'minTargets' times.", "topics": [ "screenedAtLeast" ] }, { "page": "selectiveAgainst", "title": "Identify small molecules with selective binding against a target of interest", "topics": [ "selectiveAgainst" ] }, { "page": "targetSelectivity", "title": "Returns the target selectivity for a specified list of compounds (cids).", "topics": [ "targetSelectivity" ] }, { "page": "translateTargetId", "title": "Translate a protein target identifier to another identifier system", "topics": [ "translateTargetId" ] }, { "page": "trinarySimilarity", "title": "Computes the tanimoto similarity coefficient between the bioactivity profiles of two compounds, each represented as a column in a compound vs. target sparse matrix", "topics": [ "trinarySimilarity" ] } ], "_readme": "https://github.com/bioc/bioassayR/raw/RELEASE_3_23/README.md", "_rundeps": [ "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" ], "_vignettes": [ { "source": "bioassayR.Rmd", "filename": "bioassayR.html", "title": "bioassayR Introduction and Examples", "author": "Authors: Tyler Backman, Thomas Girke", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Getting Started", "Installation", "Loading the Package and Documentation", "Quick Tutorial", "Examples", "Loading User Supplied PubChem BioAssay Data", "Prebuilt Database Example: Investigate Activity of a Known Drug", "Identify Target Selective Compounds", "Cluster Compounds by Activity Profile", "Analyze and Load Raw Screening Data", "Custom SQL Queries", "Building PubChem BioAssay Database", "Version Information", "Funding", "References" ], "created": "2015-10-07 17:52:54", "modified": "2024-10-22 04:08:22", "commits": 17 } ], "_score": 6.491641793477585, "_indexed": false, "_nocasepkg": "bioassayr", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/bioassayR", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.50.0", "date": "2026-06-07T06:48:46.000Z", "distro": "noble", "commit": "b239b42ff4e20992903b7c6fce7c665494386281", "fileid": "c16eb91b58a1ab0bc1e8b7bfd0d20e0156428d9fcbba2e3e52a1540e163e6f77", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27085191108" }, { "r": "4.6.0", "os": "linux", "version": "1.50.0", "date": "2026-06-07T06:48:46.000Z", "distro": "noble", "commit": "b239b42ff4e20992903b7c6fce7c665494386281", "fileid": "58113d772b164ecc5819a32a54e8d72852315587012f92248769f15591a206cf", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27085191108" }, { "r": "4.5.3", "os": "mac", "version": "1.50.0", "date": "2026-06-07T06:47:27.000Z", "commit": "b239b42ff4e20992903b7c6fce7c665494386281", "fileid": "28aa9fe43b668f8aa343cad432f61ef9f9cadf0949dc42275c2038aaee10b33a", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27085191108" }, { "r": "4.6.0", "os": "mac", "version": "1.50.0", "date": "2026-06-07T06:47:43.000Z", "commit": "b239b42ff4e20992903b7c6fce7c665494386281", "fileid": "ac42ab58ef5e43cc950165dbc8a53edb8ac7b1c775f2d7a36f0add592c50e21a", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27085191108" }, { "r": "4.6.0", "os": "wasm", "version": "1.50.0", "date": "2026-06-07T06:48:28.000Z", "commit": "b239b42ff4e20992903b7c6fce7c665494386281", "fileid": "20e54b353d730390b1ce64b18e6f5bb713af5717a2aa56398a4bcbfa7928edd8", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27085191108" }, { "r": "4.7.0", "os": "win", "version": "1.50.0", "date": "2026-06-07T06:47:10.000Z", "commit": "b239b42ff4e20992903b7c6fce7c665494386281", "fileid": "f4fbd86f1d2bc30b5407f513771ca0efb4da57bbcf7885479d5718d7901cced0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27085191108" }, { "r": "4.5.3", "os": "win", "version": "1.50.0", "date": "2026-06-07T06:47:02.000Z", "commit": "b239b42ff4e20992903b7c6fce7c665494386281", "fileid": "2d765b5deaa838f87717f2bcf3c8ed091d9d7c3a499190c509880b2a54820928", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27085191108" }, { "r": "4.6.0", "os": "win", "version": "1.50.0", "date": "2026-06-07T06:47:15.000Z", "commit": "b239b42ff4e20992903b7c6fce7c665494386281", "fileid": "f307f4539cdf18a6f2c97f0c58e213fdb24a672f4cb9e316bb7860ba46442f24", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27085191108" } ] }