Skip to content

@grunwaldlab Grunwald lab

Change the repository type filter

All

    Repositories list

    57 repositories

    • demulticoder

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Feb 5, 2025Feb 5, 2025

    • benchmark_demulticoder

      Public
      Scripts and associated intermediates files to accompany demulticoder manuscript
      0•0•0•0•Updated Feb 5, 2025Feb 5, 2025

    • pathogensurveillance

      Public
      Surveillance of pathogens using population genomics and sequencing
      Nextflow
      •
      MIT License
      •6•3•0•0•Updated Feb 5, 2025Feb 5, 2025

    • nextstrainoomy

      Public
      Documentation for the nextstrain software installed on the oomy webserver
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 4, 2025Feb 4, 2025

    • OomyceteDB

      Public
      A new barcode for characterizing oomycete communities.
      HTML
      •
      Other
      •1•1•14•0•Updated Jan 31, 2025Jan 31, 2025

    • pathogensurveillance_documentation

      Public
      Documentation for the pathogensurveillance pipeline
      HTML
      •
      Creative Commons Attribution Share Alike 4.0 International
      •0•0•0•0•Updated Jan 23, 2025Jan 23, 2025

    • psminer

      Public
      Work in progress. Backend for pathogensurveillance
      R
      •1•2•9•0•Updated Nov 5, 2024Nov 5, 2024

    • krisp

      Public
      A lightweight kmer-based algorithm for designing diagnostic CRISPR assays using genome data.
      Python
      •
      Other
      •3•11•21•1•Updated Aug 19, 2024Aug 19, 2024

    • aps_workshop

      Public
      MIT License
      •4•2•3•0•Updated Aug 1, 2024Aug 1, 2024

    • poppr

      Public
      🌶 An R package for genetic analysis of populations with mixed (clonal/sexual) reproduction
      population-geneticsclonalityrmultilocus-genotypesgenetic-distancesmultilocus-lineagesgenetic-analysispopulationsminimum-spanning-networks
      R
      •26•68•17•0•Updated May 16, 2024May 16, 2024

    • metacoder

      Public
      Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data
      taxonomyhierarchicaltreesmetabarcodingcranrpcrcommunity-diversity
      R
      •
      Other
      •28•137•146•0•Updated Feb 20, 2024Feb 20, 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/analysis_of_microbiome_community_data_in_r/
      HTML
      •16•17•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•10•3•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
      •749•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
      •12•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

    • Population_Genetics_in_R

      Public
      A primer for computational tools to analyze genetics of populations in R
      HTML
      •
      Other
      •51•86•11•0•Updated Feb 11, 2021Feb 11, 2021

    • GBS-Pcinnamomi

      Public
      Shell
      •3•0•0•1•Updated Feb 1, 2021Feb 1, 2021

    • vcfR

      Public
      Tools to work with variant call format files
      R
      •54•5•0•0•Updated Sep 1, 2020Sep 1, 2020

    • Supplements_Knaus_Pinfestans_CNV

      Public
      Supplements for Knaus et al. manuscript on changes variation in genic copy number in Phytophthora infestans and relatives.
      0•1•0•0•Updated May 12, 2020May 12, 2020

    • Ph_ramorum_ORforests

      Public
      Analysis of P. ramorum populations in Curry County, OR
      R
      •0•0•2•0•Updated Mar 13, 2020Mar 13, 2020

    • P_infestans_CNV

      Public
      Phytophthora infestans CNV project
      HTML
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 14, 2020Feb 14, 2020