Package: MicrobiomeBenchmarkData 1.15.1

Samuel Gamboa

MicrobiomeBenchmarkData: Datasets for benchmarking in microbiome research

The MicrobiomeBenchmarkData package provides functionality to access microbiome datasets suitable for benchmarking. These datasets have some biological truth, which allows to have expected results for comparison. The datasets come from various published sources and are provided as TreeSummarizedExperiment objects. Currently, only datasets suitable for benchmarking differential abundance methods are available.

Authors:Samuel Gamboa [aut, cre], Levi Waldron [aut], Marcel Ramos [ctb], NCI [fnd]

MicrobiomeBenchmarkData_1.15.1.tar.gz
MicrobiomeBenchmarkData_1.15.1.zip(r-4.7)MicrobiomeBenchmarkData_1.15.1.zip(r-4.6)MicrobiomeBenchmarkData_1.15.1.zip(r-4.5)
MicrobiomeBenchmarkData_1.15.1.tgz(r-4.6-any)MicrobiomeBenchmarkData_1.15.1.tgz(r-4.5-any)
MicrobiomeBenchmarkData_1.15.1.tar.gz(r-4.7-any)MicrobiomeBenchmarkData_1.15.1.tar.gz(r-4.6-any)
MicrobiomeBenchmarkData_1.15.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MicrobiomeBenchmarkData/json (API)
NEWS

# Install 'MicrobiomeBenchmarkData' in R:

install.packages('MicrobiomeBenchmarkData', repos = c('https://waldronlab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/waldronlab/microbiomebenchmarkdata/issues

Pkgdown/docs site:https://waldronlab.io

Datasets:

sampleMetadata - SampleMetadata

On CRAN:

experimentdata microbiomedata reproducibleresearch sequencingdata bioconductor-package r01ca230551

4.28 score 21 scripts 3 exports 75 dependencies

Last updated from:ed900aa65c. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	NOTE	338
source / vignettes	OK	367
linux-release-x86_64	NOTE	374
macos-release-arm64	NOTE	313
macos-oldrel-arm64	NOTE	205
windows-devel	NOTE	293
windows-release	NOTE	278
windows-oldrel	NOTE	303
wasm-release	OK	165

Exports:getBenchmarkData removeCache scml

Dependencies:abind ape askpass BH Biobase BiocFileCache BiocGenerics BiocParallel Biostrings bit bit64 blob cachem cli codetools cpp11 crayon curl DBI dbplyr DelayedArray digest dplyr fastmap filelock formatR fs futile.logger futile.options generics GenomicRanges glue httr2 IRanges jsonlite lambda.r lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats memoise nlme openssl pillar pkgconfig purrr R6 rappdirs Rcpp rlang RSQLite S4Arrays S4Vectors Seqinfo SingleCellExperiment snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tidytree treeio TreeSummarizedExperiment utf8 vctrs withr XVector yulab.utils

Datasets in MicrobiomeBenchmarkData

Samuel Gamboa

Rendered fromdatasets.Rmdusingknitr::rmarkdownon May 14 2026.

Last update: 2022-10-26
Started: 2021-09-24

MicrobiomeBenchmarkData

Samuel Gamboa, Levi Waldron

Rendered fromMicrobiomeBenchmarkData.Rmdusingknitr::rmarkdownon May 14 2026.

Last update: 2022-10-26
Started: 2021-09-07

Recalibration of the Stammler_2016_16S_spikein dataset

Samuel D. Gamboa-Tuz

Rendered fromrecalibrare_spikein_data.Rmdusingknitr::rmarkdownon May 14 2026.

Last update: 2024-09-02
Started: 2022-07-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Get dataset	getBenchmarkData
MicrobiomeBenchmarkData	MicrobiomeBenchmarkData-package MicrobiomeBenchmarkData
Remove cache	removeCache
sampleMetadata	sampleMetadata
SCML: spike-in-based calibration to total microbial load	scml