Repositories list

• pathogensurveillance

  Public
  Surveillance of pathogens using population genomics and sequencing

  HTML

  •

  MIT License

  •5•3•0•0•Updated Nov 21, 2024Nov 21, 2024

• psminer

  Public
  Work in progress. Backend for pathogensurveillance

  R

  •1•2•9•0•Updated Nov 5, 2024Nov 5, 2024

• demulticoder

  Public
  R

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  MIT License

  •0•0•0•0•Updated Oct 16, 2024Oct 16, 2024

• pathogensurveillance_documentation

  Public
  Documentation for the pathogensurveillance pipeline

  HTML

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  Creative Commons Attribution Share Alike 4.0 International

  •0•0•0•0•Updated Sep 18, 2024Sep 18, 2024

• krisp

  Public
  A lightweight kmer-based algorithm for designing diagnostic CRISPR assays using genome data.

  Python

  •

  Other

  •3•10•21•1•Updated Aug 19, 2024Aug 19, 2024

• aps_workshop

  Public
  MIT License

  •4•2•3•0•Updated Aug 1, 2024Aug 1, 2024

• OomyceteDB

  Public
  A new barcode for characterizing oomycete communities.

  HTML

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  Other

  •1•1•14•0•Updated Jun 12, 2024Jun 12, 2024

• poppr

  Public
  🌶 An R package for genetic analysis of populations with mixed (clonal/sexual) reproduction

  population-geneticsclonalityr+ 6multilocus-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

  taxonomyhierarchicaltrees+ 5metabarcodingcranrpcrcommunity-diversity

  R

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  Other

  •28•136•144•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

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  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

• nextstrainoomy

  Public
  Documentation for the nextstrain software installed on the oomy webserver

  Python

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  GNU General Public License v3.0

  •0•0•0•0•Updated Mar 14, 2023Mar 14, 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

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  MIT License

  •722•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

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  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

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  Other

  •50•85•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

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  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 14, 2020Feb 14, 2020

• MexicoPopulations

  Public
  HTML

  •1•0•0•1•Updated Apr 26, 2019Apr 26, 2019