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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/

aps_workshop

audpc_example

An example analysis for calculating AUDPC using RMarkdown

bioinformatics_practice

Record of exercises done to learn bioinformatics

coverage

Tools to explore sequencing coverage in high-throughput sequencing projects

demulticoder

effectr

An R package to call oomycete effectors

ezec

Easy Interface to Effective Concentration Calculations

gbs-pcinnamomi

gbs_data

grunwaldlab.github.io

Our home webpage for GitHub projects

idseq-workflows

Portable WDL workflows for IDseq production pipelines

krisp

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

labtools

An R package for lab notebook upkeep

metacoder

Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data

metacoder_documentation

Documentation for the metacoder R package

mexicopopulations

microbe-id

Microbe-ID

modules

Repository to host tool-specific module files for the Nextflow DSL2 community!

nextstraincommunitytest

Test repo for nextstrain community github link

nextstrainoomy

Documentation for the nextstrain software installed on the oomy webserver

oomy_rxlrs

Annotate RXLR effectors in Oomycete genomes

oomycetedb

A new barcode for characterizing oomycete communities.

oomycetedbtools

An R package for some of the code used to keep oomycetedb.org up to date.

pathogensurveillance

Surveillance of pathogens using population genomics and sequencing

pathogensurveillance_documentation

Documentation for the pathogensurveillance pipeline

ph_ramorum_orforests

Analysis of P. ramorum populations in Curry County, OR

phplurivora_or_nurseries_gbs

Publication-ready analysis and figures for Carleson et al. 201x

phytophthora_epidemiology_on_rhododendron

Data repository for a manuscript by C Taylor and NJ Grunwald.

phytophthora_id

Webpage of Phytophthora ID of the Grunwald lab.