Bioinformatics and Systems Biology Laboratory's repositories
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.
redVigilancia
Place holder for routines we use in Sars-Cov2 genome surveillance in Colombia.
rnaseq-reference
Pipeline used to analyse RNA sequencing data obtained from organisms with a reference genome and annotation
covid19-CO
Analysis of covid 19 public data in Colombia South America
GEM-multiomic-integrator
MatLab ToolBox for integration of multiple omic sources to a genome-scale metabolic model
gibbslab.github.io
GiBBS official website
Carnation_transcriptome
RNAseq data for Carnation roots Cultivars Golem and Mizuki.
GABA_reconstrucction
GABA_reconstrucction