Package: MicrobiomeBenchmarkData 1.7.1
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:
MicrobiomeBenchmarkData_1.7.1.tar.gz
MicrobiomeBenchmarkData_1.7.1.zip(r-4.5)MicrobiomeBenchmarkData_1.7.1.zip(r-4.4)MicrobiomeBenchmarkData_1.7.1.zip(r-4.3)
MicrobiomeBenchmarkData_1.7.1.tgz(r-4.4-any)MicrobiomeBenchmarkData_1.7.1.tgz(r-4.3-any)
MicrobiomeBenchmarkData_1.7.1.tar.gz(r-4.5-noble)MicrobiomeBenchmarkData_1.7.1.tar.gz(r-4.4-noble)
MicrobiomeBenchmarkData_1.7.1.tgz(r-4.4-emscripten)MicrobiomeBenchmarkData_1.7.1.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')) |
Bug tracker:https://github.com/waldronlab/microbiomebenchmarkdata/issues
- sampleMetadata - SampleMetadata
Last updated 14 days agofrom:723cb97bb5. Checks:OK: 3 NOTE: 4. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Sep 03 2024 |
R-4.5-win | NOTE | Sep 03 2024 |
R-4.5-linux | NOTE | Sep 03 2024 |
R-4.4-win | NOTE | Sep 03 2024 |
R-4.4-mac | NOTE | Sep 03 2024 |
R-4.3-win | OK | Sep 03 2024 |
R-4.3-mac | OK | Sep 03 2024 |
Exports:getBenchmarkDataremoveCachescml
Dependencies:abindapeaskpassBHBiobaseBiocFileCacheBiocGenericsBiocParallelBiostringsbitbit64blobcachemclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydigestdplyrfansifastmapfilelockformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesjsonlitelambda.rlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimenlmeopensslpillarpkgconfigplogrpurrrR6RcpprlangRSQLiteS4ArraysS4VectorsSingleCellExperimentsnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttidytreetreeioTreeSummarizedExperimentUCSC.utilsutf8vctrswithrXVectoryulab.utilszlibbioc
Datasets in MicrobiomeBenchmarkData
Rendered fromdatasets.Rmd
usingknitr::rmarkdown
on Sep 03 2024.Last update: 2022-10-26
Started: 2021-09-24
MicrobiomeBenchmarkData
Rendered fromMicrobiomeBenchmarkData.Rmd
usingknitr::rmarkdown
on Sep 03 2024.Last update: 2022-10-26
Started: 2021-09-07
Recalibration of the Stammler_2016_16S_spikein dataset
Rendered fromrecalibrare_spikein_data.Rmd
usingknitr::rmarkdown
on Sep 03 2024.Last update: 2024-09-02
Started: 2022-07-06
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 |