Package: MicrobiomeBenchmarkData 1.9.0

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]

MicrobiomeBenchmarkData_1.9.0.tar.gz
MicrobiomeBenchmarkData_1.9.0.zip(r-4.5)MicrobiomeBenchmarkData_1.9.0.zip(r-4.4)MicrobiomeBenchmarkData_1.9.0.zip(r-4.3)
MicrobiomeBenchmarkData_1.9.0.tgz(r-4.4-any)MicrobiomeBenchmarkData_1.9.0.tgz(r-4.3-any)
MicrobiomeBenchmarkData_1.9.0.tar.gz(r-4.5-noble)MicrobiomeBenchmarkData_1.9.0.tar.gz(r-4.4-noble)
MicrobiomeBenchmarkData_1.9.0.tgz(r-4.4-emscripten)MicrobiomeBenchmarkData_1.9.0.tgz(r-4.3-emscripten)
MicrobiomeBenchmarkData.pdf |MicrobiomeBenchmarkData.html✨
MicrobiomeBenchmarkData/json (API)
NEWS

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

Peer review:

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

Pkgdown site:https://waldronlab.io

Datasets:

On CRAN:

experimentdatamicrobiomedatareproducibleresearchsequencingdatabioconductor-package

4.39 score 18 scripts 3 exports 79 dependencies

Last updated 3 months agofrom:d9e18a4e0d. Checks:3 OK, 4 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 17 2025
R-4.5-winNOTEJan 17 2025
R-4.5-linuxNOTEJan 17 2025
R-4.4-winNOTEJan 17 2025
R-4.4-macNOTEJan 17 2025
R-4.3-winOKDec 18 2024
R-4.3-macOKDec 18 2024

Exports:getBenchmarkDataremoveCachescml

Dependencies:abindapeaskpassBHBiobaseBiocFileCacheBiocGenericsBiocParallelBiostringsbitbit64blobcachemclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydigestdplyrfansifastmapfilelockformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesjsonlitelambda.rlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimenlmeopensslpillarpkgconfigplogrpurrrR6RcpprlangRSQLiteS4ArraysS4VectorsSingleCellExperimentsnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttidytreetreeioTreeSummarizedExperimentUCSC.utilsutf8vctrswithrXVectoryulab.utils

Datasets in MicrobiomeBenchmarkData

Samuel Gamboa

Rendered fromdatasets.Rmdusingknitr::rmarkdownon Jan 17 2025.

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

MicrobiomeBenchmarkData

Samuel Gamboa, Levi Waldron

Rendered fromMicrobiomeBenchmarkData.Rmdusingknitr::rmarkdownon Jan 17 2025.

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 Jan 17 2025.

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

Readme and manuals

Help Manual

Help pageTopics
Get datasetgetBenchmarkData
MicrobiomeBenchmarkDataMicrobiomeBenchmarkData-package MicrobiomeBenchmarkData
Remove cacheremoveCache
sampleMetadatasampleMetadata
SCML: spike-in-based calibration to total microbial loadscml