metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data (original) (raw)
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>.
| Version: | 0.3.8 |
|---|---|
| Depends: | R (≥ 3.0.2) |
| Imports: | stringr, ggplot2, igraph, grid, taxize, seqinr, RCurl, ape, stats, grDevices, utils, lazyeval, dplyr, magrittr, readr, rlang, ggfittext, vegan, cowplot, GA, Rcpp, crayon, tibble, R6 |
| LinkingTo: | Rcpp |
| Suggests: | knitr, rmarkdown, testthat, zlibbioc, BiocManager, phyloseq, phylotate, traits, biomformat, DESeq2 |
| Published: | 2025-02-11 |
| DOI: | 10.32614/CRAN.package.metacoder |
| Author: | Zachary Foster [aut, cre], Niklaus Grunwald [ths], Kamil Slowikowski [ctb], Scott Chamberlain [ctb], Rob Gilmore [ctb] |
| Maintainer: | Zachary Foster |
| BugReports: | https://github.com/grunwaldlab/metacoder/issues |
| License: | GPL-2 | GPL-3 |
| URL: | https://grunwaldlab.github.io/metacoder_documentation/ |
| NeedsCompilation: | yes |
| Citation: | metacoder citation info |
| Materials: | README NEWS |
| In views: | Phylogenetics |
| CRAN checks: | metacoder results |
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