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-any)microSTASIS_1.12.0.zip(r-4.6-any)microSTASIS_1.12.0.zip(r-4.5-any)
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✨
DESCRIPTION |NEWS
card.svg |card.png
microSTASIS/json (API)

# 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:

geneticvariability biomedicalinformatics clustering multiplecomparison microbiome

3.48 score 2 stars 3 scripts 162 downloads 11 exports 69 dependencies

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

Target	Result	Time
bioc-checks	WARNING	155
linux-devel	ERROR	445
source / vignettes	OK	251
linux-release	ERROR	444
macos-release	ERROR	406
macos-oldrel	ERROR	481
windows-devel	ERROR	373
windows-release	ERROR	394
windows-oldrel	ERROR	341
wasm-release	OK	119

Exports:iterativeClustering iterativeClusteringCV mSerrorCV mSinternalPairedTimes mSmetadataGroups mSpreviz pairedTimes plotmSdynamics plotmSheatmap plotmSlinesCV plotmSscatter

Dependencies:abind ape BH Biobase BiocGenerics BiocParallel Biostrings cli codetools cpp11 crayon DelayedArray digest dplyr farver formatR fs futile.logger futile.options generics GenomicRanges ggplot2 ggside glue gtable IRanges isoband jsonlite labeling lambda.r lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats nlme pillar pkgconfig purrr R6 rappdirs RColorBrewer Rcpp rlang S4Arrays S4Vectors S7 scales Seqinfo SingleCellExperiment snow SparseArray stringi stringr SummarizedExperiment tibble tidyr tidyselect tidytree treeio TreeSummarizedExperiment utf8 vctrs viridisLite withr XVector yulab.utils

Introduction to microSTASIS

Rendered frommicroSTASIS.Rmdusingknitr::rmarkdown

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

Help page	Topics
Detected ASV from multiple individuals at four different sampling times.	clr
Stability of individuals after iteratively performing Hartigan-Wong k-means clustering.	iterativeClustering
Cross validation of the iterative Hartigan-Wong k-means clustering.	iterativeClusteringCV
Microbiota STability ASsessment via Iterative cluStering
Compute the mean absolute error (MAE) in percentage after 'iterativeClusteringCV()'.	mSerrorCV
Internal function for 'pairedTimes()'.	mSinternalPairedTimes
Easily extract groups of individuals from sample metadata.	mSmetadataGroups
Process the 'iterativeClustering()' output to a new format ready for the implemented visualization functions.	mSpreviz
Generate one or multiple matrices with paired times.	pairedTimes pairedTimes,matrix,matrix-method pairedTimes,matrix-method pairedTimes,TreeSummarizedExperiment,TreeSummarizedExperiment-method pairedTimes,TreeSummarizedExperiment-method
Generate boxplots of the stability dynamics throughout sampling times by groups.	plotmSdynamics
Plot a heatmap of the stability results.	plotmSheatmap
Plot the stability values after 'iterativeClusteringCV()'.	plotmSlinesCV
Plot a scatter and side boxplot of the stability results.	plotmSscatter

Package: microSTASIS 1.12.0

microSTASIS: Microbiota STability ASsessment via Iterative cluStering

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