Other packages > Find by keyword >

ReDirection  

Predict Dominant Direction of Reactions of a Biochemical Network
View on CRAN: Click here


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

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

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



Attach the package and use:
library("ReDirection")
Maintained by
Siddhartha Kundu
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2021-09-29
Latest Update: 2021-10-04
Description:
Biologically relevant, yet mathematically sound constraints are used to compute the propensity and thence infer the dominant direction of reactions of a generic biochemical network. The reactions must be unique and their number must exceed that of the reactants,i.e., reactions >= reactants + 2. 'ReDirection', computes the null space of a user-defined stoichiometry matrix. The spanning non-zero and unique reaction vectors (RVs) are combinatorially summed to generate one or more subspaces recursively. Every reaction is represented as a sequence of identical components across all RVs of a particular subspace. The terms are evaluated with (biologically relevant bounds, linear maps, tests of convergence, descriptive statistics, vector norms) and the terms are classified into forward-, reverse- and equivalent-subsets. Since, these are mutually exclusive the probability of occurrence is binary (all, 1; none, 0). The combined propensity of a reaction is the p1-norm of the sub-propensities, i.e., sum of the products of the probability and maximum numeric value of a subset (least upper bound, greatest lower bound). This, if strictly positive is the probable rate constant, is used to infer dominant direction and annotate a reaction as "Forward (f)", "Reverse (b)" or "Equivalent (e)". The inherent computational complexity (NP-hard) per iteration suggests that a suitable value for the number of reactions is around 20. Three functions comprise ReDirection. These are check_matrix() and reaction_vector() which are internal, and calculate_reaction_vector() which is external.
How to cite:
Siddhartha Kundu (2021). ReDirection: Predict Dominant Direction of Reactions of a Biochemical Network. R package version 1.0.1, https://cran.r-project.org/web/packages/ReDirection. Accessed 28 Oct. 2026.
Previous versions and publish date:
(2026-07-09 08:23), 1.0.0 (2021-09-29 10:20)
Other packages that cited ReDirection R package
View ReDirection citation profile
Other R packages that ReDirection depends, imports, suggests or enhances
Complete documentation for ReDirection
Functions, R codes and Examples using the ReDirection R package
Some associated functions: calculate_reaction_vector . check_matrix . reaction_vector . 
Some associated R codes: calculate_reaction_vector.R .  Full ReDirection package functions and examples
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

cats  
Cohort Platform Trial Simulation
Cohort plAtform Trial Simulation whereby every cohort consists of two arms, control and experimenta ...
Download / Learn more Package Citations See dependency  
nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
ncdf4  
Interface to Unidata netCDF (Version 4 or Earlier) Format Data Files
Provides a high-level R interface to data files written using Unidata's netCDF library (version 4 or ...
Download / Learn more Package Citations See dependency  
msamp  
Estimate Sample Size to Detect Bacterial Contamination in a Product Lot
Estimates the sample size needed to detect microbial contamination in a lot with a user-specified d ...
Download / Learn more Package Citations See dependency  
NPHazardRate  
Nonparametric Hazard Rate Estimation
Provides functions and examples for histogram, kernel (classical, variable bandwidth and transformat ...
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