gibbslab/GSMs

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gibbslab/GSMs

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Official Repository for Genome Scale Models created by our Team

g2f

An R package to find the gaps in metabolic networks, and fill it from the stoichiometric reactions of a reference metabolic reconstruction using a weighting function. Also include the option to download all the set of gene-associated stoichiometric reactions for a specific organism from the KEGG database.

exp2flux

An R package to incorporate in a continuous way the gene-expression data as FBA flux boundaries in a metabolic model. Also, functions to calculate and plot the differences between model fluxes in different metabolic scenarios was included. This is an implementation of the algorithm described by Lee et al. (2012) in DOI: 10.1186/1752-0509-6-73.

minval

An R package to identify orphan metabolites and evaluate the mass and charge balance of stoichiometric reactions. The package also includes functions to characterize and write models in TSV and SBML formats, extract all reactants, products, metabolite names and compartments from a metabolic reconstruction.

coexnet

An R package to build CO-EXpression NETworks from Microarray Data

rnaseq-reference

Pipeline used to analyse RNA sequencing data obtained from organisms with a reference genome and annotation

redVigilancia

Place holder for routines we use in Sars-Cov2 genome surveillance in Colombia.