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@microgenomics Microbial Genomics at CBIB

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    13 repositories

    • plotMyGBK

      Public
      Python
      •3•3•0•0•Updated Mar 8, 2023Mar 8, 2023

    • HumanMicrobiomeAnalysis

      Public
      R Shiny application accompanying the paper (unpublished) Evaluation of Computational Methods for Human Microbiome Analysis Using Simulated Data
      R
      •3•3•0•0•Updated Mar 8, 2022Mar 8, 2022

    • pasteTaxID

      Public
      This script take your fastas, search for common IDs (ti, gi, gb, emb), get the ti (or gi if is missing), and finally put the ID's in the same fasta
      Shell
      •
      GNU General Public License v2.0
      •3•6•2•0•Updated Aug 22, 2019Aug 22, 2019

    • MAGnifico

      Public
      Pipeline for metagenome-associated genome analysis (in development)
      Shell
      •1•1•0•0•Updated Jun 11, 2019Jun 11, 2019

    • tutorials

      Public
      In this repo you will find demos and tutorials prepared by members of the CBIB. Feel free to use them for non-commercial activities given that you give proper credit. Have fun!
      Python
      •
      MIT License
      •55•81•3•0•Updated Apr 1, 2018Apr 1, 2018

    • Workshop-PUC

      Public
      Repositorio para el taller de "Bioinformática: secuenciación masiva y genómica" realizado en la Universidad Católica (sede San Joaquín), Santiago, Chile. Dictado por el Dr. Eduardo Castro-Nallar, CBIB, Universidad Andres Bello. Mayo 2017
      Perl
      •
      GNU General Public License v3.0
      •5•4•0•0•Updated Sep 20, 2017Sep 20, 2017

    • MicrobiomeAnalysisData

      Public
      Files accompanying human microbiome analysis protocol
      0•0•0•0•Updated Jul 19, 2017Jul 19, 2017

    • Workshop-UTA

      Public
      Repositorio para el taller de Bioinformática a realizarse en la Universidad de Tarapacá, Arica, Chile. Dictado por el Dr. Eduardo Castro-Nallar, CBIB, Universidad Andres Bello. Mayo 2017.
      GNU General Public License v3.0
      •0•1•0•0•Updated May 25, 2017May 25, 2017

    • parseMethods

      Public
      Parse Methods Module is a Parse Module from SEPA (a multi pipe to test pathogen software detection), that parses result files from several softwares (pathoscope, metamix, sigma, metaphlan (on development), constrains (metaphlan dependent))
      Shell
      •
      GNU General Public License v2.0
      •0•2•0•0•Updated Apr 28, 2017Apr 28, 2017

    • analysisMethods

      Public
      Analysis Methods Module is a final module from SEPA ( a multi pipe to test pathogen software detection), that analyze the cvs file provided by Parse Module (or your own cvs file in particular format), the analysis aviable are R^2, RRMSE (relative error) and ROC Curve
      Shell
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Jan 27, 2017Jan 27, 2017

    • executionMethods

      Public
      execution Methods Module is the second module from SEPA (Simulation, Execution, Parse and Analysis, a multi pipe to test pathogen software detection), that take the softwares (pathoscope, metaphlan, metamix, sigma and constrains), and execute in an independent process (can be execute multiple times)
      Shell
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Jan 24, 2017Jan 24, 2017

    • simulationsMethods

      Public
      the first module of SEPA to simulate reads from genomes
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 14, 2016Nov 14, 2016

    • multiGenomicContext

      Public
      multiGenomicContext is a pipeline to see your protein in many genomic context as much as gbk you have.
      Python
      •
      GNU General Public License v3.0
      •4•0•0•0•Updated Aug 17, 2016Aug 17, 2016