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 The package can also use robust regression (unpublished work) and integrated quantile regression (Wang et al.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:Anna Plantinga [aut, cre], Nehemiah Wilson [aut, ctb], Haotian Zheng [aut, ctb], Tianying Wang [aut, ctb], Xiang Zhan [aut, ctb], Michael Wu [aut], Ni Zhao [aut, ctb], Jun Chen [aut]

MiRKAT_1.2.3.tar.gz
MiRKAT_1.2.3.zip(r-4.7)MiRKAT_1.2.3.zip(r-4.6)MiRKAT_1.2.3.zip(r-4.5)
MiRKAT_1.2.3.tgz(r-4.6-any)MiRKAT_1.2.3.tgz(r-4.5-any)
MiRKAT_1.2.3.tar.gz(r-4.7-any)MiRKAT_1.2.3.tar.gz(r-4.6-any)
MiRKAT_1.2.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MiRKAT/json (API)

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

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

5.26 score 3 stars 1 packages 201 scripts 262 downloads 30 mentions 9 exports 111 dependencies

Last updated from:7458a23464. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK216
source / vignettesOK235
linux-release-x86_64OK212
macos-release-arm64OK171
macos-oldrel-arm64OK253
windows-develOK169
windows-releaseOK179
windows-oldrelOK135
wasm-releaseOK133

Exports:D2KGLMMMiRKATKRVMiRKATMiRKAT.iQMiRKAT.QMiRKAT.RMiRKATSMMiRKAT

Dependencies:apeaskpassbase64encbootbslibcachemcliclueclustercodetoolsCompQuadFormcpp11crosstalkcurldata.tabledigestdirmultdplyrevaluatefarverfastmapfBasicsfontawesomeforeachfsgenericsggplot2ggrepelgluegssgtableGUniFrachighrhtmltoolshtmlwidgetshttrinlineisobanditeratorsjquerylibjsonlitekernlabknitrlabelinglaterlatticelazyevallifecyclelme4magrittrMASSMatrixMatrixModelsmatrixStatsmemoisemgcvmimeminqamixtoolsmodeestnlmenloptropensslotelPearsonDSpermutepillarpkgconfigplotlypromisespurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppEigenRdpackreformulasrlangrmarkdownrmutilrpartS7sassscalessegmentedSparseMspatialstablestablediststatipstatmodstringistringrsurvivalsystibbletidyrtidyselecttimeDatetimeSeriestinytexutf8vctrsveganviridisLitewithrxfunyaml

MiRKAT Package Vignette

Anna Plantinga, Nehemiah Wilson, Haotian Zheng, Xiang Zhan, Michael Wu, Jun Chen, Ni Zhao

Rendered fromMiRKAT_Vignette.Rmdusingknitr::rmarkdownon Jun 03 2026.

Last update: 2023-02-17
Started: 2020-04-14