Package: microSTASIS 1.12.0

Pedro Sánchez-Sánchez

microSTASIS: Microbiota STability ASsessment via Iterative cluStering

The toolkit 'µSTASIS', or microSTASIS, has been developed for the stability analysis of microbiota in a temporal framework by leveraging on iterative clustering. Concretely, the core function uses Hartigan-Wong k-means algorithm as many times as possible for stressing out paired samples from the same individuals to test if they remain together for multiple numbers of clusters over a whole data set of individuals. Moreover, the package includes multiple functions to subset samples from paired times, validate the results or visualize the output.

Authors:Pedro Sánchez-Sánchez [aut, cre], Alfonso Benítez-Páez [aut]

microSTASIS_1.12.0.tar.gz
microSTASIS_1.12.0.zip(r-4.7)microSTASIS_1.12.0.zip(r-4.6)microSTASIS_1.12.0.zip(r-4.5)
microSTASIS_1.12.0.tgz(r-4.6-any)microSTASIS_1.12.0.tgz(r-4.5-any)
microSTASIS_1.12.0.tar.gz(r-4.7-any)microSTASIS_1.12.0.tar.gz(r-4.6-any)
microSTASIS_1.12.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
microSTASIS/json (API)
NEWS

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

Bug tracker:https://github.com/biotechpedro/microstasis/issues

Datasets:
  • clr - Detected ASV from multiple individuals at four different sampling times.

On CRAN:

Conda:

geneticvariabilitybiomedicalinformaticsclusteringmultiplecomparisonmicrobiome

3.48 score 2 stars 4 scripts 208 downloads 11 exports 69 dependencies

Last updated from:75388f6599 (on RELEASE_3_23). Checks:1 WARNING, 7 ERROR, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING149
linux-devel-x86_64ERROR454
source / vignettesOK283
linux-release-x86_64ERROR464
macos-release-arm64ERROR428
macos-oldrel-arm64ERROR493
windows-develERROR327
windows-releaseERROR369
windows-oldrelERROR327
wasm-releaseOK139

Exports:iterativeClusteringiterativeClusteringCVmSerrorCVmSinternalPairedTimesmSmetadataGroupsmSprevizpairedTimesplotmSdynamicsplotmSheatmapplotmSlinesCVplotmSscatter

Dependencies:abindapeBHBiobaseBiocGenericsBiocParallelBiostringsclicodetoolscpp11crayonDelayedArraydigestdplyrfarverformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2ggsidegluegtableIRangesisobandjsonlitelabelinglambda.rlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsnlmepillarpkgconfigpurrrR6rappdirsRColorBrewerRcpprlangS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentsnowSparseArraystringistringrSummarizedExperimenttibbletidyrtidyselecttidytreetreeioTreeSummarizedExperimentutf8vctrsviridisLitewithrXVectoryulab.utils

Introduction to microSTASIS

Pedro Sánchez Sánchez

Rendered frommicroSTASIS.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2022-10-25
Started: 2022-09-10