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>.

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

11.03 score 72 stars 816 scripts 7.0k 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>.

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community-diversityhierarchicalmetabarcodingpcrtaxonomytreescpp

9.67 score 144 stars 411 scripts 1.3k downloads

heattree - A Self-Contained Widget for Interactive Phylogenetic Tree Visualization

Creates self-contained widgets for interactive phylogenetic tree visualization. This package wraps the 'JavaScript' 'heat-tree' package using the 'htmlwidgets' R package.

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4.11 score 2 stars 49 downloads

demulticoder - Simultaneous Analysis of Multiplexed Metabarcodes

A comprehensive set of wrapper functions for the analysis of multiplex metabarcode data. It includes robust wrappers for 'Cutadapt' and 'DADA2' to trim primers, filter reads, perform amplicon sequence variant (ASV) inference, and assign taxonomy. The package can handle single metabarcode datasets, datasets with two pooled metabarcodes, or multiple datasets simultaneously. The final output is a matrix per metabarcode, containing both ASV abundance data and associated taxonomic assignments. An optional function converts these matrices into 'phyloseq' and 'taxmap' objects. For more information on 'DADA2', including information on how 'DADA2' infers samples sequences, see Callahan et al. (2016) <doi:10.1038/nmeth.3869>. For more details on the 'demulticoder' R package see Sudermann et al. (2025) <doi:10.1094/PHYTO-02-25-0043-FI>.

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3.30 score 1 stars 1 scripts 492 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.

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2.70 score 1 stars 8 scripts 500 downloads