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 The package can also use robust regression (unpublished work) and integrated quantile regression (Wang et al.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-4.5)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'))

Peer review:

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:

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

9 exports 3 stars 3.91 score 109 dependencies 30 mentions 174 scripts 459 downloads

Last updated 2 years agofrom:7458a23464. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 30 2024
R-4.5-winOKAug 30 2024
R-4.5-linuxOKAug 30 2024
R-4.4-winOKAug 30 2024
R-4.4-macOKAug 30 2024
R-4.3-winOKJul 31 2024
R-4.3-macOKAug 30 2024

Exports:D2KGLMMMiRKATKRVMiRKATMiRKAT.iQMiRKAT.QMiRKAT.RMiRKATSMMiRKAT

Dependencies:apeaskpassbase64encbootbslibcachemcliclueclustercodetoolscolorspaceCompQuadFormcpp11crosstalkcurldata.tabledigestdirmultdplyrevaluatefansifarverfastmapfBasicsfontawesomeforeachfsgenericsggplot2ggrepelgluegssgtableGUniFrachighrhtmltoolshtmlwidgetshttrinlineisobanditeratorsjquerylibjsonlitekernlabknitrlabelinglaterlatticelazyevallifecyclelme4magrittrMASSMatrixMatrixModelsmatrixStatsmemoisemgcvmimeminqamixtoolsmodeestmunsellnlmenloptropensslPearsonDSpermutepillarpkgconfigplotlypromisespurrrquantregR6rappdirsRColorBrewerRcppRcppEigenrlangrmarkdownrmutilrpartsassscalessegmentedSparseMspatialstablestablediststatipstatmodstringistringrsurvivalsystibbletidyrtidyselecttimeDatetimeSeriestinytexutf8vctrsveganviridisLitewithrxfunyaml

MiRKAT Package Vignette

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

Rendered fromMiRKAT_Vignette.Rmdusingknitr::rmarkdownon Aug 30 2024.

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