Pinned Repositories
analysis_of_microbiome_community_data_in_r
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/
effectR
An R package to call oomycete effectors
krisp
A lightweight kmer-based algorithm for designing diagnostic CRISPR assays using genome data.
metacoder
Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data
Microbe-ID
Microbe-ID
poppr
🌶 An R package for genetic analysis of populations with mixed (clonal/sexual) reproduction
Population_Genetics_in_R
A primer for computational tools to analyze genetics of populations in R
quiltr
R package for making website representations of directories
Reproducible-science-in-R
This site provides information on conducting reproducible science using the R language.
vcfR
Tools to work with variant call format files
Grunwald lab's Repositories
grunwaldlab/metacoder
Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data
grunwaldlab/Population_Genetics_in_R
A primer for computational tools to analyze genetics of populations in R
grunwaldlab/poppr
🌶 An R package for genetic analysis of populations with mixed (clonal/sexual) reproduction
grunwaldlab/analysis_of_microbiome_community_data_in_r
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/
grunwaldlab/krisp
A lightweight kmer-based algorithm for designing diagnostic CRISPR assays using genome data.
grunwaldlab/effectR
An R package to call oomycete effectors
grunwaldlab/vcfR
Tools to work with variant call format files
grunwaldlab/pathogensurveillance
Surveillance of pathogens using population genomics and sequencing
grunwaldlab/aps_workshop
grunwaldlab/metacoder_documentation
Documentation for the metacoder R package
grunwaldlab/psminer
Work in progress. Backend for pathogensurveillance
grunwaldlab/bioinformatics_practice
Record of exercises done to learn bioinformatics
grunwaldlab/idseq-workflows
Portable WDL workflows for IDseq production pipelines
grunwaldlab/OomyceteDB
A new barcode for characterizing oomycete communities.
grunwaldlab/Supplements_Knaus_Pinfestans_CNV
Supplements for Knaus et al. manuscript on changes variation in genic copy number in Phytophthora infestans and relatives.
grunwaldlab/demulticoder
grunwaldlab/NextstrainCommunityTest
Test repo for nextstrain community github link
grunwaldlab/nextstrainoomy
Documentation for the nextstrain software installed on the oomy webserver
grunwaldlab/oomy_RXLRs
Annotate RXLR effectors in Oomycete genomes
grunwaldlab/pathogensurveillance_documentation
Documentation for the pathogensurveillance pipeline
grunwaldlab/GBS-Pcinnamomi
grunwaldlab/MexicoPopulations
grunwaldlab/modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
grunwaldlab/oomycetedbtools
An R package for some of the code used to keep oomycetedb.org up to date.
grunwaldlab/P_infestans_CNV
Phytophthora infestans CNV project
grunwaldlab/Ph_ramorum_ORforests
Analysis of P. ramorum populations in Curry County, OR
grunwaldlab/Phytophthora_epidemiology_on_Rhododendron
Data repository for a manuscript by C Taylor and NJ Grunwald.
grunwaldlab/Pram_pacbio_EU1_NA1
Genome data associated with an MPMI Genome Announcement for Phytophthora ramorum EU1 and NA1 genomes
grunwaldlab/rps10_barcode
Analysis code for "A new oomycete metabarcoding method using the rps10 gene"
grunwaldlab/scylv
Nextstrain analysis of Sugarcane yellow leaf virus