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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 |
| Reference manual: | metacoder.pdf |
| Vignettes: |
Documentation for metacoder (source) |
| Package source: | metacoder_0.3.8.tar.gz |
| Windows binaries: | r-devel: metacoder_0.3.8.zip, r-release: metacoder_0.3.8.zip, r-oldrel: metacoder_0.3.8.zip |
| macOS binaries: | r-devel (arm64): metacoder_0.3.8.tgz, r-release (arm64): metacoder_0.3.8.tgz, r-oldrel (arm64): metacoder_0.3.8.tgz, r-devel (x86_64): metacoder_0.3.8.tgz, r-release (x86_64): metacoder_0.3.8.tgz, r-oldrel (x86_64): metacoder_0.3.8.tgz |
| Old sources: | metacoder archive |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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