rbiom: Read/Write, Analyze, and Visualize 'BIOM' Data (original) (raw)
A toolkit for working with Biological Observation Matrix ('BIOM') files. Read/write all 'BIOM' formats. Compute rarefaction, alpha diversity, and beta diversity (including 'UniFrac'). Summarize counts by taxonomic level. Subset based on metadata. Generate visualizations and statistical analyses. CPU intensive operations are coded in C for speed.
| Version: | 2.2.0 |
|---|---|
| Depends: | R (≥ 4.2.0) |
| Imports: | methods, mgcv, stats, utils, ape, dplyr, emmeans, fillpattern, ggbeeswarm, ggnewscale, ggplot2, ggrepel, ggtext, jsonlite, magrittr, parallelly, patchwork, pillar, plyr, readr, readxl, slam, vegan |
| Suggests: | cli, crayon, ggdensity, glue, labeling, lifecycle, openxlsx, optparse, pkgconfig, prettycode, R6, rlang, scales, testthat, tibble, tsne, uwot |
| Published: | 2025-04-04 |
| DOI: | 10.32614/CRAN.package.rbiom |
| Author: | Daniel P. Smith  [aut, cre], Alkek Center for Metagenomics and Microbiome Research [cph, fnd] |
| Maintainer: | Daniel P. Smith |
| BugReports: | https://github.com/cmmr/rbiom/issues |
| License: | MIT + file |
| URL: | https://cmmr.github.io/rbiom/, https://github.com/cmmr/rbiom |
| NeedsCompilation: | yes |
| Materials: | README |
| CRAN checks: | rbiom results |
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