Package: adaptiveGPCA 0.1.3

adaptiveGPCA: Adaptive Generalized PCA

Implements adaptive gPCA, as described in: Fukuyama, J. (2017) <arxiv:1702.00501>. The package also includes functionality for applying the method to 'phyloseq' objects so that the method can be easily applied to microbiome data and a 'shiny' app for interactive visualization.

Authors:Julia Fukuyama [aut, cre]

adaptiveGPCA_0.1.3.tar.gz
adaptiveGPCA_0.1.3.zip(r-4.5)adaptiveGPCA_0.1.3.zip(r-4.4)adaptiveGPCA_0.1.3.zip(r-4.3)
adaptiveGPCA_0.1.3.tgz(r-4.4-any)adaptiveGPCA_0.1.3.tgz(r-4.3-any)
adaptiveGPCA_0.1.3.tar.gz(r-4.5-noble)adaptiveGPCA_0.1.3.tar.gz(r-4.4-noble)
adaptiveGPCA_0.1.3.tgz(r-4.4-emscripten)adaptiveGPCA_0.1.3.tgz(r-4.3-emscripten)
adaptiveGPCA.pdf |adaptiveGPCA.html✨
adaptiveGPCA/json (API)

# Install 'adaptiveGPCA' in R:

install.packages('adaptiveGPCA', repos = c('https://jfukuyama.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jfukuyama/adaptivegpca/issues

Datasets:

AntibioticPhyloseq - Antibiotic time course experiment.
AntibioticSmall - A subset of the antibiotic data

On CRAN:

5.33 score 9 stars 24 scripts 322 downloads 2 mentions 8 exports 92 dependencies

Last updated 2 years agofrom:a93a3334e3. Checks:OK: 6 WARNING: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 04 2024
R-4.5-win	OK	Nov 04 2024
R-4.5-linux	WARNING	Nov 04 2024
R-4.4-win	OK	Nov 04 2024
R-4.4-mac	OK	Nov 04 2024
R-4.3-win	OK	Nov 04 2024
R-4.3-mac	OK	Nov 04 2024

Exports:adaptivegpca estimateComponents gpca gpcaFullFamily inspectTaxonomy processPhyloseq varianceOnEvecs visualizeFullFamily

Dependencies:ade4 ape askpass base64enc Biobase BiocGenerics biomformat Biostrings bslib cachem cli cluster codetools colorspace commonmark cpp11 crayon curl data.table digest fansi farver fastmap fontawesome foreach fs generics GenomeInfoDb GenomeInfoDbData ggplot2 glue gtable htmltools httpuv httr igraph IRanges isoband iterators jquerylib jsonlite labeling later lattice lifecycle magrittr MASS Matrix memoise mgcv mime multtest munsell nlme openssl permute phyloseq pillar pixmap pkgconfig plyr promises R6 rappdirs RColorBrewer Rcpp RcppArmadillo reshape2 rhdf5 rhdf5filters Rhdf5lib rlang S4Vectors sass scales shiny sourcetools sp stringi stringr survival sys tibble UCSC.utils utf8 vctrs vegan viridisLite withr xtable XVector zlibbioc

adaptiveGPCA vignette

Julia Fukuyama

Rendered fromadaptive_gpca_vignette.Rmdusingknitr::rmarkdownon Nov 04 2024.

Last update: 2018-03-14
Started: 2016-06-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
adaptiveGPCA: A package for structured dimensionality reduction	adaptiveGPCA-package
Adaptive gPCA	adaptivegpca
Antibiotic time course experiment.	AntibioticPhyloseq
A subset of the antibiotic data	AntibioticSmall
Estimate parameters in hierarchical model	estimateComponents
gPCA	gpca
Make a sequence of ordinations	gpcaFullFamily
Shiny gadget for tree/taxonomy inspection	inspectTaxonomy
Plot an adaptivegpca object	plot.adaptivegpca
Print an adaptivegpca object	print.adaptivegpca
Make the input matrices for adaptive gPCA	processPhyloseq
Variance along eigenvectors of Q	varianceOnEvecs
Shiny gadget for adaptive gPCA	visualizeFullFamily