Microbial Genomics at CBIB
This is the Github site for the Microbial Genomics lab at the CBIB
Santiago - Chile
Pinned Repositories
analysisMethods
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
executionMethods
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)
HumanMicrobiomeAnalysis
R Shiny application accompanying the paper (unpublished) Evaluation of Computational Methods for Human Microbiome Analysis Using Simulated Data
MAGnifico
Pipeline for metagenome-associated genome analysis (in development)
parseMethods
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))
pasteTaxID
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
plotMyGBK
tutorials
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!
Workshop-PUC
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
Workshop-UTA
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.
Microbial Genomics at CBIB's Repositories
microgenomics/tutorials
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!
microgenomics/pasteTaxID
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
microgenomics/Workshop-PUC
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
microgenomics/HumanMicrobiomeAnalysis
R Shiny application accompanying the paper (unpublished) Evaluation of Computational Methods for Human Microbiome Analysis Using Simulated Data
microgenomics/plotMyGBK
microgenomics/parseMethods
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))
microgenomics/MAGnifico
Pipeline for metagenome-associated genome analysis (in development)
microgenomics/Workshop-UTA
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.
microgenomics/analysisMethods
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
microgenomics/executionMethods
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)
microgenomics/MicrobiomeAnalysisData
Files accompanying human microbiome analysis protocol
microgenomics/multiGenomicContext
multiGenomicContext is a pipeline to see your protein in many genomic context as much as gbk you have.
microgenomics/simulationsMethods
the first module of SEPA to simulate reads from genomes