Package: smoke 2.0.1

smoke: Small Molecule Octet/BLI Kinetics Experiment

Bio-Layer Interferometry (BLI) is a technology to determine the binding kinetics between biomolecules. BLI signals are small and noisy when small molecules are investigated as ligands (analytes). We develop this package to process and analyze the BLI data acquired on Octet Red96 from Fortebio more accurately. Sun Q., Li X., et al (2020) <doi:10.1038/s41467-019-14238-3>. In this new version, we organize the BLI experiment data and analysis methods into a S4 class with self-explaining structure.

Authors:Qingan Sun, Xiaojun Li, James C Sacchettini

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

Peer review:

Datasets:
  • bli - BLI data example

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.00 score 145 downloads 23 exports 2 dependencies

Last updated 8 months agofrom:033ff7a331. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 06 2024
R-4.5-winOKNov 06 2024
R-4.5-linuxOKNov 06 2024
R-4.4-winOKNov 06 2024
R-4.4-macOKNov 06 2024
R-4.3-winOKNov 06 2024
R-4.3-macOKNov 06 2024

Exports:alignLoadbaselineBlidoubleBlankestimatefitKineticsinitializekineticskOff0kOff0<-kOn0kOn0<-ligandligand<-plotKineticsplotResidualsplotTracesshowstatustExptExp<-tracestraces<-

Dependencies:rbibutilsRdpack

Readme and manuals

Help Manual

Help pageTopics
Small Molecule Octet/BLI Kinetics Experimentsmoke-package smoke
Align BLI traces with loading stepalignLoad
~~ Methods for Function 'alignLoad' ~~alignLoad,Bli-method alignLoad-methods
Align BLI traces with baseline stepbaseline
~~ Methods for Function 'baseline' ~~baseline,Bli-method baseline-methods
BLI data examplebli
Constructor of "Bli" classBli
Class '"Bli"'Bli-class
Substract the double-referencesdoubleBlank
~~ Methods for Function 'doubleBlank' ~~doubleBlank,Bli-method doubleBlank-methods
Estimate initial kinetic parametersestimate
~~ Methods for Function 'estimate' ~~estimate,Bli-method estimate-methods
Fit binding kineticsfitKinetics
~~ Methods for Function 'fitKinetics' ~~fitKinetics,Bli-method fitKinetics-methods
~~ Methods for Function 'initialize' ~~initialize,Bli-method initialize-methods
Output kinetics modelkinetics
~~ Methods for Function 'kinetics' ~~kinetics,Bli-method kinetics-methods
Getter for "Bli" slot of 'kOff0'kOff0
~~ Methods for Function 'kOff0' ~~kOff0,Bli-method kOff0-methods
Setter for "Bli" slot of 'kOff0'kOff0<-
~~ Methods for Function 'kOff0<-' ~~kOff0<-,Bli-method kOff0<--methods
Getter for "Bli" slot of 'kOn0'kOn0
~~ Methods for Function 'kOn0' ~~kOn0,Bli-method kOn0-methods
Setter for "Bli" slot of 'kOn0'kOn0<-
~~ Methods for Function 'kOn0<-' ~~kOn0<-,Bli-method kOn0<--methods
Getter for "Bli" slot of ligand concentrationligand
~~ Methods for Function 'ligand' ~~ligand,Bli-method ligand-methods
Setter for "Bli" slot of ligand concentrationligand<-
~~ Methods for Function 'ligand<-' ~~ligand<-,Bli-method ligand<--methods
Class 'nls'nls-class
Plot kinetics model fittingplotKinetics
~~ Methods for Function 'plotKinetics' ~~plotKinetics,Bli-method plotKinetics-methods
Plot residuals from kinetics model fittingplotResiduals
~~ Methods for Function 'plotResiduals' ~~plotResiduals,Bli-method plotResiduals-methods
Plot BLI tracesplotTraces
~~ Methods for Function 'plotTraces' ~~plotTraces,Bli-method plotTraces-methods
~~ Methods for Function 'show' ~~show,Bli-method show-methods
Getter for data processing 'status'status
~~ Methods for Function 'status' ~~status,Bli-method status-methods
Getter for BLI times 'tExp'tExp
~~ Methods for Function 'tExp' ~~tExp,Bli-method tExp-methods
Setter for BLI times 'tExp'tExp<-
~~ Methods for Function 'tExp<-' ~~tExp<-,Bli-method tExp<--methods
Getter of BLI 'traces'traces
~~ Methods for Function 'traces' ~~traces,Bli-method traces-methods
Setter of BLI 'traces'traces<-
~~ Methods for Function 'traces<-' ~~traces<-,Bli-method traces<--methods