poppr - Genetic Analysis of Populations with Mixed Reproduction

Population genetic analyses for hierarchical analysis of partially clonal populations built upon the architecture of the 'adegenet' package. Originally described in Kamvar, Tabima, and Grünwald (2014) <doi:10.7717/peerj.281> with version 2.0 described in Kamvar, Brooks, and Grünwald (2015) <doi:10.3389/fgene.2015.00208>.

Last updated 10 months ago

clonalitygenetic-analysisgenetic-distancesminimum-spanning-networksmultilocus-genotypesmultilocus-lineagespopulation-geneticspopulationsopenmp

10.70 score 68 stars 672 scripts 5.6k downloads

metacoder - Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

Reads, plots, and manipulates large taxonomic data sets, like those generated from modern high-throughput sequencing, such as metabarcoding (i.e. amplification metagenomics, 16S metagenomics, etc). It provides a tree-based visualization called "heat trees" used to depict statistics for every taxon in a taxonomy using color and size. It also provides various functions to do common tasks in microbiome bioinformatics on data in the 'taxmap' format defined by the 'taxa' package. The 'metacoder' package is described in the publication by Foster et al. (2017) <doi:10.1371/journal.pcbi.1005404>.

Last updated 26 days ago

community-diversityhierarchicalmetabarcodingpcrtaxonomytreescpp

9.61 score 138 stars 328 scripts 188 downloads

ezec - Easy Interface to Effective Concentration Calculations

Because fungicide resistance is an important phenotypic trait for fungi and oomycetes, it is necessary to have a standardized method of statistically analyzing the Effective Concentration (EC) values. This package is designed for those who are not terribly familiar with R to be able to analyze and plot an entire set of isolates using the 'drc' package.

Last updated 9 years ago

3.70 score 1 stars 6 scripts 176 downloads