grunwaldlab/Reproducible-science-in-R

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grunwaldlab/Reproducible-science-in-R

grunwaldlab

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This site provides information on conducting reproducible science using the R language.

metacoder

Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data

Population_Genetics_in_R

A primer for computational tools to analyze genetics of populations in R

poppr

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

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/

krisp

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

effectR

An R package to call oomycete effectors

quiltr

R package for making website representations of directories

Microbe-ID

aps_workshop

audpc_example

An example analysis for calculating AUDPC using RMarkdown

psminer

Work in progress. Backend for pathogensurveillance

supplementary-poppr-2.0

Supplementary materials for Frontiers paper on novel R tools for population genomics

metacoder_documentation

Documentation for the metacoder R package

popgen_review_examples

Examples for population genetics review manuscript

phytophthora_id

Webpage of Phytophthora ID of the Grunwald lab.

ezec

Easy Interface to Effective Concentration Calculations

labtools

An R package for lab notebook upkeep

Supplements_Knaus_Pinfestans_CNV

Supplements for Knaus et al. manuscript on changes variation in genic copy number in Phytophthora infestans and relatives.

OomyceteDB

A new barcode for characterizing oomycete communities.

poppr-poster-aps-2016

source data for the APS 2016 poster on Tools for analysis of clonal population genetic data in R

bioinformatics_practice

Record of exercises done to learn bioinformatics