{ "_id": "6ad1f1ebd3c80a766859c974", "Package": "smoke", "Type": "Package", "Title": "Small Molecule Octet/BLI Kinetics Experiment", "Version": "2.0.1", "Date": "2024-03-11", "Author": "Qingan Sun, Xiaojun Li, James C Sacchettini", "Maintainer": "Qingan Sun ", "Description": "Bio-Layer Interferometry (BLI) is a technology to\ndetermine the binding kinetics between biomolecules. BLI\nsignals are small and noisy when small molecules are\ninvestigated as ligands (analytes). We develop this package to\nprocess and analyze the BLI data acquired on Octet Red96 from\nFortebio more accurately. Sun Q., Li X., et al (2020)\n. In this new version, we\norganize the BLI experiment data and analysis methods into a S4\nclass with self-explaining structure.", "License": "GPL-2 | GPL-3", "RdMacros": "Rdpack", "LazyData": "true", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-16 09:11:49 UTC", "User": "root" }, "Repository": "https://quinsun.r-universe.dev", "Date/Publication": "2024-03-11 02:32:53 UTC", "RemoteUrl": "https://github.com/cran/smoke", "RemoteRef": "HEAD", "RemoteSha": "033ff7a3310056ccfe3a51dff3a5f5b467d452ff", "_user": "quinsun", "_type": "src", "_file": "smoke_2.0.1.tar.gz", "_fileid": "https://r2.ropensci.org/d03e6331d246c4cc6db11c2e37348d005bbaeae1a31bf683279b66c6d5863165", "_filesize": 1391872, "_sha256": "d03e6331d246c4cc6db11c2e37348d005bbaeae1a31bf683279b66c6d5863165", "_expires": "2027-01-24T09:44:09.000Z", "_created": "2026-10-16T09:11:49.000Z", "_published": "2026-10-16T09:44:11.471Z", "_buildurl": "https://github.com/r-universe/quinsun/actions/runs/38878483463", "_status": 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"_stars": 0, "_contributors": [ { "user": "quinsun", "count": 3, "uuid": 58658490 } ], "_userbio": { "uuid": 58658490, "type": "user", "name": "quinsun", "followers": 0 }, "_downloads": { "count": 221, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/smoke" }, "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/smoke.html" ], "_realowner": "quinsun", "_cranurl": false, "_releases": [ { "version": "1.0.1", "date": "2019-12-16" }, { "version": "2.0.0", "date": "2020-01-19" }, { "version": "2.0.1", "date": "2024-03-10" } ], "_exports": [ "alignLoad", "baseline", "Bli", "doubleBlank", "estimate", "fitKinetics", "initialize", "kinetics", "kOff0", "kOff0<-", "kOn0", "kOn0<-", "ligand", "ligand<-", "plotKinetics", "plotResiduals", "plotTraces", "show", "status", "tExp", "tExp<-", "traces", "traces<-" ], "_datasets": [ { "name": "bli", "title": "BLI data example", "object": "bli", "class": [ "Bli" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "smoke-package", "title": "Small Molecule Octet/BLI Kinetics Experiment", "topics": [ "smoke-package", "smoke" ] }, { "page": "alignLoad", "title": "Align BLI traces with loading step", "topics": [ "alignLoad" ] }, { "page": "alignLoad-methods", "title": "~~ Methods for Function 'alignLoad' ~~", "topics": [ "alignLoad,Bli-method", "alignLoad-methods" ] }, { "page": "baseline", "title": "Align BLI traces with baseline step", "topics": [ "baseline" ] }, { "page": "baseline-methods", "title": "~~ Methods for Function 'baseline' ~~", "topics": [ "baseline,Bli-method", "baseline-methods" ] }, { "page": "bliData", "title": "BLI data example", "topics": [ "bli" ] }, { "page": "Bli", "title": "Constructor of \"Bli\" class", "topics": [ "Bli" ] }, { "page": "Bli-class", "title": "Class '\"Bli\"'", "topics": [ "Bli-class" ] }, { "page": "doubleBlank", "title": "Substract the double-references", "topics": [ "doubleBlank" ] }, { "page": "doubleBlank-methods", "title": "~~ Methods for Function 'doubleBlank' ~~", "topics": [ "doubleBlank,Bli-method", "doubleBlank-methods" ] }, { "page": "estimate", "title": "Estimate initial kinetic parameters", "topics": [ "estimate" ] }, { "page": "estimate-methods", "title": "~~ Methods for Function 'estimate' ~~", "topics": [ "estimate,Bli-method", "estimate-methods" ] }, { "page": "fitKinetics", "title": "Fit binding kinetics", "topics": [ "fitKinetics" ] }, { "page": "fitKinetics-methods", "title": "~~ Methods for Function 'fitKinetics' ~~", "topics": [ "fitKinetics,Bli-method", "fitKinetics-methods" ] }, { "page": "initialize-methods", "title": "~~ Methods for Function 'initialize' ~~", "topics": [ "initialize,Bli-method", "initialize-methods" ] }, { "page": "kinetics", "title": "Output kinetics model", "topics": [ "kinetics" ] }, { "page": "kinetics-methods", "title": "~~ Methods for Function 'kinetics' ~~", "topics": [ "kinetics,Bli-method", "kinetics-methods" ] }, { "page": "kOff0", "title": "Getter for \"Bli\" slot of 'kOff0'", "topics": [ "kOff0" ] }, { "page": "kOff0-methods", "title": "~~ Methods for Function 'kOff0' ~~", "topics": [ "kOff0,Bli-method", "kOff0-methods" ] }, { "page": "kOff0_-", "title": "Setter for \"Bli\" slot of 'kOff0'", "topics": [ "kOff0<-" ] }, { "page": "kOff0_--methods", "title": "~~ Methods for Function 'kOff0<-' ~~", "topics": [ "kOff0<-,Bli-method", "kOff0<--methods" ] }, { "page": "kOn0", "title": "Getter for \"Bli\" slot of 'kOn0'", "topics": [ "kOn0" ] }, { "page": "kOn0-methods", "title": "~~ Methods for Function 'kOn0' ~~", "topics": [ "kOn0,Bli-method", "kOn0-methods" ] }, { "page": "kOn0_-", "title": "Setter for \"Bli\" slot of 'kOn0'", "topics": [ "kOn0<-" ] }, { "page": "kOn0_--methods", "title": "~~ Methods for Function 'kOn0<-' ~~", "topics": [ "kOn0<-,Bli-method", "kOn0<--methods" ] }, { "page": "ligand", "title": "Getter for \"Bli\" slot of ligand concentration", "topics": [ "ligand" ] }, { "page": "ligand-methods", "title": "~~ Methods for Function 'ligand' ~~", "topics": [ "ligand,Bli-method", "ligand-methods" ] }, { "page": "ligand_-", "title": "Setter for \"Bli\" slot of ligand concentration", "topics": [ "ligand<-" ] }, { "page": "ligand_--methods", "title": "~~ Methods for Function 'ligand<-' ~~", "topics": [ "ligand<-,Bli-method", "ligand<--methods" ] }, { "page": "nls-class", "title": "Class 'nls'", "topics": [ "nls-class" ] }, { "page": "plotKinetics", "title": "Plot kinetics model fitting", "topics": [ "plotKinetics" ] }, { "page": "plotKinetics-methods", "title": "~~ Methods for Function 'plotKinetics' ~~", "topics": [ "plotKinetics,Bli-method", "plotKinetics-methods" ] }, { "page": "plotResiduals", "title": "Plot residuals from kinetics model fitting", "topics": [ "plotResiduals" ] }, { "page": "plotResiduals-methods", "title": "~~ Methods for Function 'plotResiduals' ~~", "topics": [ "plotResiduals,Bli-method", "plotResiduals-methods" ] }, { "page": "plotTraces", "title": "Plot BLI traces", "topics": [ "plotTraces" ] }, { "page": "plotTraces-methods", "title": "~~ Methods for Function 'plotTraces' ~~", "topics": [ "plotTraces,Bli-method", "plotTraces-methods" ] }, { "page": "show-methods", "title": "~~ Methods for Function 'show' ~~", "topics": [ "show,Bli-method", "show-methods" ] }, { "page": "status", "title": "Getter for data processing 'status'", "topics": [ "status" ] }, { "page": "status-methods", "title": "~~ Methods for Function 'status' ~~", "topics": [ "status,Bli-method", "status-methods" ] }, { "page": "tExp", "title": "Getter for BLI times 'tExp'", "topics": [ "tExp" ] }, { "page": "tExp-methods", "title": "~~ Methods for Function 'tExp' ~~", "topics": [ "tExp,Bli-method", "tExp-methods" ] }, { "page": "tExp_-", "title": "Setter for BLI times 'tExp'", "topics": [ "tExp<-" ] }, { "page": "tExp_--methods", "title": "~~ Methods for Function 'tExp<-' ~~", 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