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 <zacharyfoster1989 at gmail.com> |
| 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 |