Package: MiSPU 1.0

Chong Wu

MiSPU: Microbiome Based Sum of Powered Score (MiSPU) Tests

There is an increasing interest in investigating how the compositions of microbial communities are associated with human health and disease. In this package, we present a novel global testing method called aMiSPU, that is highly adaptive and thus high powered across various scenarios, alleviating the issue with the choice of a phylogenetic distance. Our simulations and real data analysis demonstrated that aMiSPU test was often more powerful than several competing methods while correctly controlling type I error rates.

Authors:Chong Wu, Wei Pan

MiSPU_1.0.tar.gz
MiSPU_1.0.tar.gz(r-4.5-noble)MiSPU_1.0.tar.gz(r-4.4-noble)
MiSPU_1.0.tgz(r-4.4-emscripten)MiSPU_1.0.tgz(r-4.3-emscripten)
MiSPU.pdf |MiSPU.html
MiSPU/json (API)

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

Peer review:

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:
  • dd - The estimate of Dirichlet-multinomial distribution
  • throat.meta - Meta data of the throat microbiome samples.
  • throat.otu.tab - OTU count table from 16S sequencing of the throat microbiome samples.
  • throat.tree - UPGMA tree of the OTUs from 16S sequencing of the throat microbiome samples.

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

openblascpp

2.06 score 19 scripts 146 downloads 6 mentions 6 exports 21 dependencies

Last updated 9 years agofrom:a72fd26cf3. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-linux-x86_64OKNov 29 2024

Exports:correspLeavesGUniFracMiSPUrankingrdirichletsimulateData

Dependencies:apeaSPUclusterdigestdotCall64fieldsgeelatticemapsMASSMatrixmatrixStatsmgcvmvtnormnlmepermuteRcppRcppArmadillospamveganviridisLite