conjugator: conjugator: A package to compute conjugation rate estimates

In JSHuisman/conjugator: Estimate Plasmid Conjugation Rates

Description

The conjugator package provides the functions for conjugation rate estimation, the assessment of critical times, and basic growth rate estimation. Details about these methods can be found in Huisman et al., 2020 https://www.biorxiv.org/content/10.1101/2020.03.09.980862v1

Details

This functionality can also be explored in a Shiny app, available at https://ibz-shiny.ethz.ch/jhuisman/conjugator/.

Conjugation rate estimation

The estimate_conj_rate function allows the user to compute a variety of conjugation rate estimates from experimental data. Currently implemented are the Simonsen and Approximate Simonsen endpoint formulae, T/D, T/DR, T/(T+R), as well as T/sqrt(DR) and log(T/sqrt(DR)) (called Dionisio and Gama, respectively).

Critical time estimation

The applicability of the formulae to assess conjugation rates breaks down once transconjugants become the dominant source of conjugation event, and once the recipient population is depleted by conjugation. Each of these processes determines a "critical time". We offer functions to estimate these critical times from experimental data.

Growth rate estimation

The package also contains some basic functions to estimate population growth rates from OD data. This is for convenience, and only in service of the conjugation rate estimation. We take no responsibility for the correctness of the growth results, and generally recommend using a specialized package (e.g. growthcurver) for this purpose.

JSHuisman/conjugator documentation built on Dec. 18, 2021, 12:27 a.m.