rbiom: Read/Write, Analyze, and Visualize 'BIOM' Data
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 <dansmith01 at gmail.com> |
| BugReports: | https://github.com/cmmr/rbiom/issues |
| License: | MIT + file LICENSE |
| URL: | https://cmmr.github.io/rbiom/, https://github.com/cmmr/rbiom |
| NeedsCompilation: | yes |
| Materials: | README |
| CRAN checks: | rbiom results |
Documentation:
| Reference manual: | rbiom.pdf |
Downloads:
| Package source: | rbiom_2.2.0.tar.gz |
| Windows binaries: | r-devel: rbiom_2.2.0.zip, r-release: rbiom_2.2.0.zip, r-oldrel: rbiom_2.2.0.zip |
| macOS binaries: | r-release (arm64): rbiom_2.2.0.tgz, r-oldrel (arm64): rbiom_2.2.0.tgz, r-release (x86_64): rbiom_2.2.0.tgz, r-oldrel (x86_64): rbiom_2.2.0.tgz |
| Old sources: | rbiom archive |
Reverse dependencies:
| Reverse imports: | mia |
Linking:
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