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

Datasets:

On CRAN:

experimentdatamicrobiomedatareproducibleresearchsequencingdatabioconductor-package

4.69 score 36 scripts 3 exports 80 dependencies

Last updated 24 days agofrom:d9e18a4e0d. Checks:OK: 3 WARNING: 1 NOTE: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 18 2024
R-4.5-winNOTENov 18 2024
R-4.5-linuxWARNINGNov 18 2024
R-4.4-winNOTENov 18 2024
R-4.4-macNOTENov 18 2024
R-4.3-winOKNov 18 2024
R-4.3-macOKNov 18 2024

Exports:getBenchmarkDataremoveCachescml

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

Datasets in MicrobiomeBenchmarkData

Samuel Gamboa

Rendered fromdatasets.Rmdusingknitr::rmarkdownon Nov 18 2024.

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

MicrobiomeBenchmarkData

Samuel Gamboa, Levi Waldron

Rendered fromMicrobiomeBenchmarkData.Rmdusingknitr::rmarkdownon Nov 18 2024.

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 Nov 18 2024.

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