Package: renz 0.2.1

renz: R-Enzymology

Contains utilities for the analysis of Michaelian kinetic data. Beside the classical linearization methods (Lineweaver-Burk, Eadie-Hofstee, Hanes-Woolf and Eisenthal-Cornish-Bowden), features include the ability to carry out weighted regression analysis that, in most cases, substantially improves the estimation of kinetic parameters (Aledo (2021) <doi:10.1002/bmb.21522>). To avoid data transformation and the potential biases introduced by them, the package also offers functions to directly fitting data to the Michaelis-Menten equation, either using ([S], v) or (time, [S]) data. Utilities to simulate substrate progress-curves (making use of the Lambert W function) are also provided. The package is accompanied of vignettes that aim to orientate the user in the choice of the most suitable method to estimate the kinetic parameter of an Michaelian enzyme.

Authors:Juan Carlos Aledo

renz_0.2.1.tar.gz
renz_0.2.1.zip(r-4.7-any)renz_0.2.1.zip(r-4.6-any)renz_0.2.1.zip(r-4.5-any)
renz_0.2.1.tgz(r-4.6-any)renz_0.2.1.tgz(r-4.5-any)
renz_0.2.1.tar.gz(r-4.7-any)renz_0.2.1.tar.gz(r-4.6-any)
renz_0.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
renz/json (API)

# Install 'renz' in R:
install.packages('renz', repos = c('https://jcaledo.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • hk - Kinetic data for the phosphorylation of glucose catalyzed by hexokinase.
  • ONPG - Kinetic data for the hydrolysis of ONPG catalyzed by Beta-galactosidase
  • TcTS - Kinetic data for Trypanosoma cruzi trans-sialidase.

On CRAN:

Conda:

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

4.17 score 59 scripts 267 downloads 9 exports 1 dependencies

Last updated from:baea88b5b1. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK125
source / vignettesOK167
linux-release-x86_64OK127
macos-release-arm64OK153
macos-oldrel-arm64OK188
windows-develOK83
windows-releaseOK72
windows-oldrelOK101
wasm-releaseOK104

Exports:bibidir.MMecbehfE.progresshwint.MMlbsE.progress

Dependencies:VGAM

Fitting the Michaelis-Menten Model
Non-linear least square | Loading some real kinetic data | First thing first: scatter plot | Direct Michaelis-Menten fitting
Rendered fromdirMM.Rmdusingknitr::rmarkdown

Last update: 2023-11-28
Started: 2021-12-02

Michaelis-Menten and the Lambert W function
Stating the problem we want to solve | The integrated Michaelis-Menten | The Lambert W function | Fitting the progress curve for enzyme-catalyzed reactions
Rendered fromLambert.Rmdusingknitr::rmarkdown

Last update: 2023-11-28
Started: 2021-12-02

Enzyme Kinetic Parameters
Introduction
Rendered fromKm_Vm.Rmdusingknitr::rmarkdown

Last update: 2021-12-02
Started: 2021-12-02

Integrated Michaelis-Menten Equation
How many progress-curves do we need to estimate $K_m$ and $V_{max}$? | Integrating the Michaelis-Menten equation | Some final considerations
Rendered fromintMM.Rmdusingknitr::rmarkdown

Last update: 2021-12-02
Started: 2021-12-02

Linearized Michaelis-Menten Equations
Loading kinetic data | First thing first: scatter plot | Linearizing the Michaelis-Menten equation | Lineweaver-Burk | Hanes-Woolf | Eadie-Hofstee | Eisenthal & Cornish-Bowden
Rendered fromLinearized_MM.Rmdusingknitr::rmarkdown

Last update: 2021-12-02
Started: 2021-12-02