Skip to content

@grunwaldlab Grunwald lab

Change the repository type filter

All

    Repositories list

    63 repositories

    • heattree

      Public
      A wrapper for the javascript `heat-tree` package for interactive phylogenetic tree visualization widgets
      R
      •
      Other
      •0•2•3•0•Updated Apr 24, 2026Apr 24, 2026

    • pathogensurveillance_publications

      Public
      Documentation for the pathogensurveillance pipeline
      HTML
      •
      Other
      •0•0•0•0•Updated Apr 23, 2026Apr 23, 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•7•0•Updated Apr 16, 2026Apr 16, 2026

    • heattree_py

      Public
      Interactive phylogenetic tree visualisation for Python and Jupyter notebooks.
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 16, 2026Apr 16, 2026

    • metacoder

      Public
      Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data
      cranrtaxonomy
      cranrtaxonomyhierarchicaltreespcrmetabarcodingcommunity-diversity
      R
      •
      Other
      •29•144•44•0•Updated Apr 10, 2026Apr 10, 2026

    • oomy_RXLRs

      Public
      Annotate RXLR effectors in Oomycete genomes
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Apr 9, 2026Apr 9, 2026

    • pathogensurveillance

      Public
      Surveillance of pathogens using population genomics and sequencing
      Nextflow
      •
      MIT License
      •6•4•0•0•Updated Apr 5, 2026Apr 5, 2026

    • PathoSurveilR

      Public
      Tools to find and manipulate the output of pathogensurveillance
      R
      •
      Other
      •1•3•5•0•Updated Mar 11, 2026Mar 11, 2026

    • ezec

      Public
      Easy Interface to Effective Concentration Calculations
      R
      •1•1•2•1•Updated Mar 9, 2026Mar 9, 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

    • 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

    • 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
      •1k•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
    ProTip! When viewing an organization's repositories, you can use the props. filter to filter by custom property.