Public Health Bioinformatics

Repositories

• snakemake_demo
  Jupyter Notebook MIT 0 0 0 0 Updated Jan 21, 2021

• irida-plugin-tbprofiler

  tuberculosis antimicrobial-resistance irida-pipeline
  Java Apache-2.0 1 0 1 2 Updated Jan 21, 2021

• decision-tree

  A question and answer web form system for exploring the research questions and datasets pertinent to an emerging infectious disease outbreak.
  Makefile 1 0 0 0 Updated Jan 15, 2021

• DataHarmonizer
  JavaScript MIT 0 5 7 0 Updated Dec 19, 2020

• irida-plugin-snippy-single

  Call SNPs and indels between a reference genome and your sequence data
  Java 0 0 2 0 Updated Nov 20, 2020

• irida-plugin-snippy-phylogenomics

  Call core SNPs agains a reference genome for a set of bacterial isolates, and build a phylogenetic tree based on the core-genome SNP information.

  bioinformatics-pipeline microbial-genomics phylogenomics-pipeline irida-pipeline
  Java 1 1 3 1 Updated Nov 20, 2020

• COVID19-QC
  Python MIT 0 0 0 0 Updated Nov 10, 2020

• irida-plugin-plasmid-screen

  bioinformatics-pipeline galaxy antimicrobial-resistance irida-pipeline plasmid-genomics
  Java 0 0 1 1 Updated Oct 13, 2020

• irida-plugin-tetyper

  Determine the sequence type of specific transposable elements in bacterial isolates.

  bioinformatics-pipeline microbial-genomics galaxy transposable-elements irida-pipeline
  Java Apache-2.0 0 0 1 1 Updated Oct 13, 2020

• irida-plugin-species-abundance

  Estimate the relative abundance of sequence reads originating from different species in a sample using the IRIDA system

  metagenomics bioinformatics-pipeline microbial-genomics species-abundance-distributions species-identification irida-pipeline
  Java Apache-2.0 0 0 2 1 Updated Oct 13, 2020

• irida-plugin-resistance-screen

  Detect the presence of specific resistance genes in a sample using the IRIDA system

  bioinformatics-pipeline microbial-genomics antimicrobial-resistance irida-pipelines
  Java Apache-2.0 2 0 1 1 Updated Oct 13, 2020

• pubmlst_client

  List and download schemes from pubMLST.org and other BIGSDB servers

  bioinformatics mlst rest-client
  Python MIT 3 6 0 0 Updated Oct 5, 2020

• LexMapr

  LexMapr: A Lexicon and Rule-Based Tool for Translating Short Biomedical Specimen Descriptions into Semantic Web Ontology Terms
  Python GPL-3.0 5 6 1 2 Updated Aug 20, 2020

• lexmapr_ontology

  An ontology that contains various agency category schemes that Lexmapr can use to report matched terms by.
  CC0-1.0 1 0 0 1 Updated Aug 10, 2020

• ontofetch

  Ontofetch is a command line tool to fetch branches of terms from a given local file or internet based ontology URL. This is output in JSON format, and includes term label, definition, broad, narrow, exact and unspecified) synonyms.
  Python 0 1 1 0 Updated Jun 24, 2020

• galaxy_tools

  tools genomics microbial-genomics usegalaxy genomic-workflows
  Python 1 0 0 0 Updated Mar 26, 2020

• irida-plugin-micall-lite

  Human RNA virus genotyping

  bioinformatics-pipeline galaxy viral-genomics irida-pipeline
  Java Apache-2.0 0 0 1 0 Updated Feb 28, 2020

• blast_reporting

  A Galaxy tool that converts an NCBI BLAST XML format search result into 12, 24, 26 or custom column tabular and HTML reports.
  Python AFL-3.0 2 1 2 1 Updated Feb 27, 2020

• purl.obolibrary.org

  Forked from OBOFoundry/purl.obolibrary.org

  A new system for managing OBO PURLs
  Python BSD-3-Clause 77 0 0 0 Updated Dec 20, 2019

• tutorial

  Protege tutorial resources
  0 1 0 0 Updated Nov 15, 2019

• flu_classification_suite

  💉 📊 Flu Classification Suite
  Python 0 2 2 0 Updated Nov 12, 2019

• irida-plugin-mlst

  Determine the MLST sequence type for samples using PubMLST schemes in the IRIDA system

  bioinformatics-pipeline microbial-genomics mlst galaxy irida-pipeline microbial-subtyping
  Java 2 0 1 0 Updated Jun 20, 2019

• cpo-pipeline

  An analysis pipeline for the purpose of investigating Carbapenemase-Producing Organisms.
  Python MIT 2 1 8 0 Updated Jun 14, 2019

• sequdas-qc
  Python MIT 2 0 1 1 Updated Apr 30, 2019

• software-development-best-practices
  0 0 0 0 Updated Apr 2, 2019

• irida

  Forked from phac-nml/irida

  Canada’s Integrated Rapid Infectious Disease Analysis Platform for Genomic Epidemiology
  Java Apache-2.0 27 0 0 0 Updated Mar 20, 2019

• sequdas-web
  Python MIT 0 1 3 1 Updated Mar 20, 2019

• clade_assignment

  Python scripts to assign clade designations to influenza amino acid fasta files.
  Python 2 0 0 0 Updated Jan 8, 2019

• routine-nanopore-processing
  Shell GPL-3.0 1 0 1 0 Updated Jan 3, 2019

• sequdas-uploader
  Python MIT 0 0 0 0 Updated Dec 4, 2018