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smoke (version 2.0.1)

Small Molecule Octet/BLI Kinetics Experiment

Description

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) . In this new version, we organize the BLI experiment data and analysis methods into a S4 class with self-explaining structure.

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Version

Install

install.packages('smoke')

Monthly Downloads

128

Version

2.0.1

License

GPL-2 | GPL-3

Maintainer

Qingan Sun

Last Published

March 10th, 2024

Functions in smoke (2.0.1)

Getter for "Bli" slot of kOff0

~~ Methods for Function kOn0<- ~~

Getter for "Bli" slot of ligand concentration

Plot kinetics model fitting

plotResiduals-methods

~~ Methods for Function plotResiduals ~~

fitKinetics-methods

~~ Methods for Function fitKinetics ~~

Estimate initial kinetic parameters

Plot BLI traces

traces<--methods

~~ Methods for Function traces<- ~~

plotKinetics-methods

~~ Methods for Function plotKinetics ~~

~~ Methods for Function show ~~

Getter for data processing status

Setter of BLI traces

ligand<--methods

~~ Methods for Function ligand<- ~~

Getter of BLI traces

Setter for "Bli" slot of ligand concentration

Setter for BLI times tExp

tools:::Rd_package_title("smoke")

~~ Methods for Function tExp ~~

~~ Methods for Function traces ~~

Setter for "Bli" slot of kOn0

~~ Methods for Function status ~~

kinetics-methods

~~ Methods for Function kinetics ~~

plotTraces-methods

~~ Methods for Function plotTraces ~~

Plot residuals from kinetics model fitting

Output kinetics model

~~ Methods for Function tExp<- ~~

Getter for BLI times tExp

doubleBlank-methods

~~ Methods for Function doubleBlank ~~

Align BLI traces with baseline step

Constructor of "Bli" class

BLI data example

Substract the double-references

initialize-methods

~~ Methods for Function initialize ~~

baseline-methods

~~ Methods for Function baseline ~~

Fit binding kinetics

estimate-methods

~~ Methods for Function estimate ~~

~~ Methods for Function ligand ~~

~~ Methods for Function kOff0 ~~

Getter for "Bli" slot of kOn0

~~ Methods for Function kOn0 ~~

alignLoad-methods

~~ Methods for Function alignLoad ~~

kOff0<--methods

~~ Methods for Function kOff0<- ~~

Align BLI traces with loading step

Setter for "Bli" slot of kOff0