Other packages > Find by keyword >

TemporalGSSA  

Outputs Temporal Profile of Molecules from Stochastic Simulation Algorithm Generated Datasets
View on CRAN: Click here


Download and install TemporalGSSA package within the R console
Install from CRAN:
install.packages("TemporalGSSA")

Install from Github:
library("remotes")
install_github("cran/TemporalGSSA")

Install by package version:
library("remotes")
install_version("TemporalGSSA", "1.0.1")



Attach the package and use:
library("TemporalGSSA")
Maintained by
Siddhartha Kundu
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2022-03-02
Latest Update: 2022-10-09
Description:
The data that is generated from independent and consecutive 'GillespieSSA' runs for a generic biochemical network is formatted as rows and constitutes an observation. The first column of each row is the computed timestep for each run. Subsequent columns are used for the number of molecules of each participating molecular species or "metabolite" of a generic biochemical network. In this way 'TemporalGSSA', is a wrapper for the R-package 'GillespieSSA'. The number of observations must be at least 30. This will generate data that is statistically significant. 'TemporalGSSA', transforms this raw data into a simulation time-dependent and metabolite-specific trial. Each such trial is defined as a set of linear models (n >= 30) between a timestep and number of molecules for a metabolite. Each linear model is characterized by coefficients such as the slope, arbitrary constant, etc. The user must enter an integer from 1-4. These specify the statistical modality utilized to compute a representative timestep (mean, median, random, all). These arguments are mandatory and will be checked. Whilst, the numeric indicator "0" indicates suitability, "1" prompts the user to revise and re-enter their data. An optional logical argument controls the output to the console with the default being "TRUE" (curtailed) whilst "FALSE" (verbose). The coefficients of each linear model are averaged (mean slope, mean constant) and are incorporated into a metabolite-specific linear regression model as the dependent variable. The independent variable is the representative timestep chosen previously. The generated data is the imputed molecule number for an in silico experiment with (n >=30) observations. These steps can be replicated with multiple set of observations. The generated "technical replicates" can be statistically evaluated (mean, standard deviation) and will constitute simulation time-dependent molecules for each metabolite. For SSA-generated datasets with varying simulation times 'TemporalGSSA' will generate a simulation time-dependent trajectory for each metabolite of the biochemical network under study. The relevant publication with the mathematical derivation of the algorithm is (2022, Journal of Bioinformatics and Computational Biology) <doi:10.1142/S0219720022500184>. The algorithm has been deployed in the following publications (2021, Heliyon) <doi:10.1016/j.heliyon.2021.e07466> and (2016, Journal of Theoretical Biology) <doi:10.1016/j.jtbi.2016.07.002>.
How to cite:
Siddhartha Kundu (2022). TemporalGSSA: Outputs Temporal Profile of Molecules from Stochastic Simulation Algorithm Generated Datasets. R package version 1.0.1, https://cran.r-project.org/web/packages/TemporalGSSA. Accessed 27 Oct. 2026.
Previous versions and publish date:
(2026-07-09 08:27), 1.0.0 (2022-03-02 09:50)
Other packages that cited TemporalGSSA R package
View TemporalGSSA citation profile
Other R packages that TemporalGSSA depends, imports, suggests or enhances
Complete documentation for TemporalGSSA
Functions, R codes and Examples using the TemporalGSSA R package
Some associated functions: calculate_TemporalGSSA . check_TemporalGSSA . 
Some associated R codes: calculate_TemporalGSSA.R .  Full TemporalGSSA package functions and examples
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

spanish  
Translate Quantities from Strings to Integer and Back. Misc Functions on Spanish Data
Character vector to numerical translation in Euros from Spanish spelled monetary quantities. Reverse ...
Download / Learn more Package Citations See dependency  
r2resize  
In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency  
SGB  
Simplicial Generalized Beta Regression
Main properties and regression procedures using a generalization of the Dirichlet distribution calle ...
Download / Learn more Package Citations See dependency  
exams2learnr  
Interface for 'exams' Exercises in 'learnr' Tutorials
Automatic generation of quizzes or individual questions for 'learnr' tutorials based on 'R/exams' ex ...
Download / Learn more Package Citations See dependency  
usemodels  
Boilerplate Code for 'Tidymodels' Analyses
Code snippets to fit models using the tidymodels framework can be easily created for a given data se ...
Download / Learn more Package Citations See dependency  

29,218

R Packages

247,686

Dependencies

77,281

Author Associations

29,219

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA