Repositories list

• GABA_reconstrucction

  Public
  GABA_reconstrucction

  MATLAB

  •0•0•0•0•Updated Sep 11, 2024Sep 11, 2024

• GSMs

  Public
  Official Repository for Genome Scale Models created by our Team

  1•1•0•0•Updated Sep 11, 2024Sep 11, 2024

• Carnation_transcriptome

  Public
  RNAseq data for Carnation roots Cultivars Golem and Mizuki.

  0•0•0•0•Updated Apr 19, 2024Apr 19, 2024

• golemdata

  Public
  RNAseq data for golem sequencing.

  0•0•0•0•Updated Apr 29, 2023Apr 29, 2023

• rnaseq-reference

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

  Shell

  •1•1•0•1•Updated Sep 26, 2022Sep 26, 2022

• fetch_NGS

  Public
  Pipeline to fetch metadata and raw FastQ files from different databases

  Shell

  •1•0•0•0•Updated Sep 26, 2022Sep 26, 2022

• biobash

  Public
  Common BASH routines for computational biology

  bashbioinformaticstranscriptomics+ 5bioinformatics-analysisbioinformatics-scriptsbash-scriptinggenomic-data-analysisbioinformatics-tool

  Shell

  •

  MIT License

  •3•3•0•0•Updated May 23, 2022May 23, 2022

• minval

  Public
  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.

  bioinformaticsmetabolismmass-balance+ 6metabolic-modelscharge-balancesbmlcranstoichiometric-reactionsminval

  R

  •1•2•0•0•Updated May 18, 2022May 18, 2022

• GEM-multiomic-integrator

  Public
  MatLab ToolBox for integration of multiple omic sources to a genome-scale metabolic model

  MATLAB

  •0•0•0•0•Updated Apr 12, 2022Apr 12, 2022

• vigilant

  Public
  Pipeline for the assembly and analysis of SARS-CoV2 genomes in Colombia

  Shell

  •1•0•0•0•Updated Nov 20, 2021Nov 20, 2021

• redVigilancia

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

  Shell

  •0•1•0•0•Updated Aug 17, 2021Aug 17, 2021

• g2f

  Public
  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.

  bioinformaticsmetabolismreactions+ 4gapstoichiometric-reactionsmetabolic-networkfill-gaps

  R

  •3•5•1•1•Updated Dec 5, 2020Dec 5, 2020

• gibbslab.github.io

  Public
  GiBBS official website

  HTML

  •0•0•0•0•Updated Oct 26, 2020Oct 26, 2020

• GTP

  Public
  GiBBS Tuxedo Pipeline.

  0•0•0•0•Updated Apr 25, 2020Apr 25, 2020

• covid19-CO

  Public
  Analysis of covid 19 public data in Colombia South America

  Python

  •3•0•0•0•Updated Apr 20, 2020Apr 20, 2020

• topoTest

  Public
  topoTest: An R package to do random distribution and robustness tests based on network topology.

  R

  •0•0•0•0•Updated Sep 4, 2018Sep 4, 2018

• coexnet

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

  R

  •1•1•3•0•Updated Jul 10, 2018Jul 10, 2018

• exp2flux

  Public
  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.

  bioinformaticsgene-expressionmetabolism+ 4metabolic-modelsmetabolic-networkflux-balance-analysisfba-fluxes

  R

  •0•3•0•0•Updated May 2, 2017May 2, 2017