Package: MiRKAT 1.2.3
MiRKAT: Microbiome Regression-Based Kernel Association Tests
Test for overall association between microbiome composition data and phenotypes via phylogenetic kernels. The phenotype can be univariate continuous or binary (Zhao et al. (2015) <doi:10.1016/j.ajhg.2015.04.003>), survival outcomes (Plantinga et al. (2017) <doi:10.1186/s40168-017-0239-9>), multivariate (Zhan et al. (2017) <doi:10.1002/gepi.22030>) and structured phenotypes (Zhan et al. (2017) <doi:10.1111/biom.12684>). The package can also use robust regression (unpublished work) and integrated quantile regression (Wang et al. (2021) <doi:10.1093/bioinformatics/btab668>). In each case, the microbiome community effect is modeled nonparametrically through a kernel function, which can incorporate phylogenetic tree information.
Authors:
MiRKAT_1.2.3.tar.gz
MiRKAT_1.2.3.zip(r-4.5)MiRKAT_1.2.3.zip(r-4.4)MiRKAT_1.2.3.zip(r-4.3)
MiRKAT_1.2.3.tgz(r-4.4-any)MiRKAT_1.2.3.tgz(r-4.3-any)
MiRKAT_1.2.3.tar.gz(r-4.5-noble)MiRKAT_1.2.3.tar.gz(r-4.4-noble)
MiRKAT_1.2.3.tgz(r-4.4-emscripten)MiRKAT_1.2.3.tgz(r-4.3-emscripten)
MiRKAT.pdf |MiRKAT.html✨
MiRKAT/json (API)
# Install 'MiRKAT' in R: |
install.packages('MiRKAT', repos = c('https://aplantin.r-universe.dev', 'https://cloud.r-project.org')) |
- bindata - Simulated DEPENDENT data with BINOMIAL traits for correlated regression-based analysis
- nordata - Simulated DEPENDENT data with GAUSSIAN traits for correlated regression-based analysis
- poisdata - Simulated DEPENDENT data with POISSON
- throat.meta - Simulated metadata for microbiome regression-based analysis
- throat.otu.tab - Simulated OTU data for microbiome regression analysis
- throat.tree - Simulated rooted phylogenetic tree
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 years agofrom:7458a23464. Checks:OK: 7. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Oct 29 2024 |
R-4.5-win | OK | Oct 29 2024 |
R-4.5-linux | OK | Oct 29 2024 |
R-4.4-win | OK | Oct 29 2024 |
R-4.4-mac | OK | Oct 29 2024 |
R-4.3-win | OK | Oct 29 2024 |
R-4.3-mac | OK | Oct 29 2024 |
Exports:D2KGLMMMiRKATKRVMiRKATMiRKAT.iQMiRKAT.QMiRKAT.RMiRKATSMMiRKAT
Dependencies:apeaskpassbase64encbootbslibcachemcliclueclustercodetoolscolorspaceCompQuadFormcpp11crosstalkcurldata.tabledigestdirmultdplyrevaluatefansifarverfastmapfBasicsfontawesomeforeachfsgenericsggplot2ggrepelgluegssgtableGUniFrachighrhtmltoolshtmlwidgetshttrinlineisobanditeratorsjquerylibjsonlitekernlabknitrlabelinglaterlatticelazyevallifecyclelme4magrittrMASSMatrixMatrixModelsmatrixStatsmemoisemgcvmimeminqamixtoolsmodeestmunsellnlmenloptropensslPearsonDSpermutepillarpkgconfigplotlypromisespurrrquantregR6rappdirsRColorBrewerRcppRcppEigenrlangrmarkdownrmutilrpartsassscalessegmentedSparseMspatialstablestablediststatipstatmodstringistringrsurvivalsystibbletidyrtidyselecttimeDatetimeSeriestinytexutf8vctrsveganviridisLitewithrxfunyaml