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DESCRIPTION
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DESCRIPTION
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Package: rbiom
Type: Package
Title: Read/Write, Analyze, and Visualize 'BIOM' Data
Version: 2.0.0.9137
Date: 2024-08-06
Authors@R: c(
person("Daniel P.", "Smith", , "[email protected]", role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-2479-2044")),
person("Alkek Center for Metagenomics and Microbiome Research", role = c("cph", "fnd"))
)
Maintainer: Daniel P. Smith <[email protected]>
Description:
A toolkit for working with Biological Observation Matrix ('BIOM') files.
Features include reading/writing all 'BIOM' formats, rarefaction, alpha
diversity, beta diversity (including 'UniFrac'), summarizing counts by
taxonomic level, subsetting, visualizations, and statistical analysis.
All CPU intensive operations are written in C.
URL: https://cmmr.github.io/rbiom/, https://github.com/cmmr/rbiom
BugReports: https://github.com/cmmr/rbiom/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.2.0)
Additional_repositories: https://cmmr.github.io/rbiom
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Config/Needs/website: rmarkdown
Config/testthat/edition: 3
Config/testthat/parallel: true
LinkingTo:
Rcpp,
RcppParallel
Imports:
cluster,
methods,
mgcv,
stats,
utils,
ape,
broom,
dplyr,
emmeans,
ggbeeswarm,
ggnewscale,
ggplot2,
ggrepel,
ggtext,
jsonlite,
magrittr,
patchwork,
pillar,
plyr,
RcppParallel,
R.utils,
slam,
vegan
Suggests:
Biostrings,
cli,
crayon,
ggdensity,
fillpattern,
glue,
npregfast,
labeling,
lifecycle,
openxlsx,
optparse,
phyloseq,
pkgconfig,
prettycode,
R6,
ragg,
reshape2,
rhdf5,
rlang,
scales,
SummarizedExperiment,
testthat,
tibble,
TreeSummarizedExperiment,
tsne,
uwot,
vdiffr