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    62 repositories

    • pathogensurveillance

      Public
      Surveillance of pathogens using population genomics and sequencing
      Nextflow
      •
      MIT License
      •6•4•0•0•Updated Mar 2, 2026Mar 2, 2026

    • ezec

      Public
      Easy Interface to Effective Concentration Calculations
      R
      •1•1•2•1•Updated Feb 28, 2026Feb 28, 2026

    • metaMapWidgetR

      Public
      R package wrapping meta-map-widget
      R
      •
      Other
      •0•0•2•0•Updated Feb 27, 2026Feb 27, 2026

    • meta-map-widget

      Public
      Map widget for the PathogenSurveillance pipeline
      JavaScript
      •
      Other
      •0•0•2•0•Updated Feb 16, 2026Feb 16, 2026

    • heattree

      Public
      A wrapper for the javascript `heat-tree` package for interactive phylogenetic tree visualization widgets
      R
      •0•0•2•0•Updated Feb 11, 2026Feb 11, 2026

    • heat-tree

      Public
      A self-contained widget for phylogenetic and taxonomic tree visualization with categorical and continuous variables associated with nodes and tips
      JavaScript
      •0•0•4•0•Updated Feb 10, 2026Feb 10, 2026

    • PathoSurveilR

      Public
      Tools to find and manipulate the output of pathogensurveillance
      R
      •
      Other
      •1•3•5•0•Updated Feb 9, 2026Feb 9, 2026

    • metacoder

      Public
      Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data
      cranrtaxonomy
      cranrtaxonomyhierarchicaltreespcrmetabarcodingcommunity-diversity
      R
      •
      Other
      •29•144•46•0•Updated Feb 6, 2026Feb 6, 2026

    • pathogensurveillance_publications

      Public
      Documentation for the pathogensurveillance pipeline
      HTML
      •
      Other
      •0•0•0•0•Updated Feb 2, 2026Feb 2, 2026

    • aquisilvae_and_rhizoterrae_description

      Public
      Analyses used in the description of the new species Globisporangium aquisilvae and Globisporangium rhizoterrae
      R
      •0•0•0•0•Updated Jan 5, 2026Jan 5, 2026

    • SuddenOakDeathSurveillance

      Public
      Phylogeographic Monitoring of Sudden Oak Death Pathogen using Nextstrain
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 17, 2025Sep 17, 2025

    • poppr

      Public
      🌶 An R package for genetic analysis of populations with mixed (clonal/sexual) reproduction
      rmultilocus-genotypesgenetic-distances
      rmultilocus-genotypesgenetic-distancespopulation-geneticsmultilocus-lineagesgenetic-analysispopulationsminimum-spanning-networksclonality
      R
      •26•72•17•0•Updated Sep 10, 2025Sep 10, 2025

    • demulticoder

      Public
      R
      •
      Other
      •0•1•2•0•Updated Jun 13, 2025Jun 13, 2025

    • benchmark_demulticoder

      Public
      Scripts and associated intermediates files to accompany demulticoder manuscript
      0•0•0•0•Updated Mar 27, 2025Mar 27, 2025

    • aps_workshop

      Public
      MIT License
      •4•2•3•0•Updated Feb 14, 2025Feb 14, 2025

    • OomyceteDB

      Public
      A new barcode for characterizing oomycete communities.
      HTML
      •
      Other
      •1•1•11•0•Updated Jan 31, 2025Jan 31, 2025

    • krisp

      Public
      A lightweight kmer-based algorithm for designing diagnostic CRISPR assays using genome data.
      Python
      •
      Other
      •3•13•22•1•Updated Aug 19, 2024Aug 19, 2024

    • bioinformatics_practice

      Public
      Record of exercises done to learn bioinformatics
      R
      •0•1•0•0•Updated Feb 8, 2024Feb 8, 2024

    • analysis_of_microbiome_community_data_in_r

      Public
      This is the source code for the "Analysis of Microbiome Community Data in R" ICPP 2018 workshop. The website is available at: https://grunwaldlab.github.io/ana…
      HTML
      •14•16•3•0•Updated Nov 30, 2023Nov 30, 2023

    • oomy_RXLRs

      Public
      Annotate RXLR effectors in Oomycete genomes
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 31, 2023Aug 31, 2023

    • effectR

      Public
      An R package to call oomycete effectors
      R
      •7•11•2•0•Updated Aug 31, 2023Aug 31, 2023

    • metacoder_documentation

      Public
      Documentation for the metacoder R package
      HTML
      •2•2•7•0•Updated Oct 26, 2022Oct 26, 2022

    • modules

      Public
      Repository to host tool-specific module files for the Nextflow DSL2 community!
      Nextflow
      •
      MIT License
      •972•0•0•0•Updated Sep 22, 2022Sep 22, 2022

    • scylv

      Public
      Nextstrain analysis of Sugarcane yellow leaf virus
      Python
      •1•0•0•0•Updated Sep 14, 2022Sep 14, 2022

    • rps10_barcode

      Public
      Analysis code for "A new oomycete metabarcoding method using the rps10 gene"
      R
      •1•0•1•0•Updated Apr 5, 2022Apr 5, 2022

    • oomycetedbtools

      Public
      An R package for some of the code used to keep oomycetedb.org up to date.
      R
      •0•0•0•0•Updated Feb 9, 2022Feb 9, 2022

    • Pram_pacbio_EU1_NA1

      Public
      Genome data associated with an MPMI Genome Announcement for Phytophthora ramorum EU1 and NA1 genomes
      0•0•0•0•Updated Dec 15, 2021Dec 15, 2021

    • idseq-workflows

      Public
      Portable WDL workflows for IDseq production pipelines
      Python
      •
      MIT License
      •11•1•0•0•Updated Dec 8, 2021Dec 8, 2021

    • NextstrainCommunityTest

      Public
      Test repo for nextstrain community github link
      0•0•0•0•Updated Aug 24, 2021Aug 24, 2021

    • Phytophthora_epidemiology_on_Rhododendron

      Public
      Data repository for a manuscript by C Taylor and NJ Grunwald.
      0•0•0•0•Updated Mar 16, 2021Mar 16, 2021