Bioinformatics and Systems Biology Laboratory
Institute for Genetics - Universidad Nacional de Colombia
Bogotá, Colombia
Pinned Repositories
biobash
Common BASH routines for computational biology
coexnet
An R package to build CO-EXpression NETworks from Microarray Data
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.
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.
GEM-multiomic-integrator
MatLab ToolBox for integration of multiple omic sources to a genome-scale metabolic model
gibbslab.github.io
GiBBS official website
GSMs
Official Repository for Genome Scale Models created by our Team
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
Bioinformatics and Systems Biology Laboratory's Repositories
gibbslab/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.
gibbslab/biobash
Common BASH routines for computational biology
gibbslab/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.
gibbslab/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.
gibbslab/coexnet
An R package to build CO-EXpression NETworks from Microarray Data
gibbslab/GSMs
Official Repository for Genome Scale Models created by our Team
gibbslab/redVigilancia
Place holder for routines we use in Sars-Cov2 genome surveillance in Colombia.
gibbslab/rnaseq-reference
Pipeline used to analyse RNA sequencing data obtained from organisms with a reference genome and annotation
gibbslab/fetch_NGS
Pipeline to fetch metadata and raw FastQ files from different databases
gibbslab/GEM-multiomic-integrator
MatLab ToolBox for integration of multiple omic sources to a genome-scale metabolic model
gibbslab/gibbslab.github.io
GiBBS official website
gibbslab/golemdata
RNAseq data for golem sequencing.
gibbslab/GTP
GiBBS Tuxedo Pipeline.
gibbslab/topoTest
topoTest: An R package to do random distribution and robustness tests based on network topology.
gibbslab/vigilant
Pipeline for the assembly and analysis of SARS-CoV2 genomes in Colombia
gibbslab/Carnation_transcriptome
RNAseq data for Carnation roots Cultivars Golem and Mizuki.
gibbslab/covid19-CO
Analysis of covid 19 public data in Colombia South America