Package: microSTASIS 1.7.0

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_1.7.0.tar.gz
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microSTASIS_1.7.0.tgz(r-4.4-any)microSTASIS_1.7.0.tgz(r-4.3-any)
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microSTASIS.pdf |microSTASIS.html✨
microSTASIS/json (API)
NEWS

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

Peer review:

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

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

On BioConductor:microSTASIS-1.5.0(bioc 3.20)microSTASIS-1.4.0(bioc 3.19)

geneticvariabilitybiomedicalinformaticsclusteringmultiplecomparisonmicrobiome

4.30 score 2 stars 1 scripts 118 downloads 11 exports 81 dependencies

Last updated 17 days agofrom:cc85111e30. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 30 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 30 2024
R-4.4-macNOTEOct 30 2024
R-4.3-winNOTEOct 30 2024
R-4.3-macNOTEOct 30 2024

Exports:iterativeClusteringiterativeClusteringCVmSerrorCVmSinternalPairedTimesmSmetadataGroupsmSprevizpairedTimesplotmSdynamicsplotmSheatmapplotmSlinesCVplotmSscatter

Dependencies:abindapeaskpassBHBiobaseBiocGenericsBiocParallelBiostringsclicodetoolscolorspacecpp11crayoncurlDelayedArraydigestdplyrfansifarverformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggsidegluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigpurrrR6RColorBrewerRcpprlangS4ArraysS4VectorsscalesSingleCellExperimentsnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttidytreetreeioTreeSummarizedExperimentUCSC.utilsutf8vctrsviridisLitewithrXVectoryulab.utilszlibbioc

Introduction to microSTASIS

Pedro Sánchez Sánchez

Rendered frommicroSTASIS.Rmdusingknitr::rmarkdownon Oct 30 2024.

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