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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 21 Nov. 2024.
Previous versions and publish date:
1.0.0 (2021-09-29 10:20)
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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
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