Package: phyloseqGraphTest 0.1.1

phyloseqGraphTest: Graph-Based Permutation Tests for Microbiome Data

Provides functions for graph-based multiple-sample testing and visualization of microbiome data, in particular data stored in 'phyloseq' objects. The tests are based on those described in Friedman and Rafsky (1979) <http://www.jstor.org/stable/2958919>, and the tests are described in more detail in Callahan et al. (2016) <doi:10.12688/f1000research.8986.1>.

Authors:Julia Fukuyama [aut, cre]

phyloseqGraphTest_0.1.1.tar.gz
phyloseqGraphTest_0.1.1.zip(r-4.5)phyloseqGraphTest_0.1.1.zip(r-4.4)phyloseqGraphTest_0.1.1.zip(r-4.3)
phyloseqGraphTest_0.1.1.tgz(r-4.4-any)phyloseqGraphTest_0.1.1.tgz(r-4.3-any)
phyloseqGraphTest_0.1.1.tar.gz(r-4.5-noble)phyloseqGraphTest_0.1.1.tar.gz(r-4.4-noble)
phyloseqGraphTest_0.1.1.tgz(r-4.4-emscripten)phyloseqGraphTest_0.1.1.tgz(r-4.3-emscripten)
phyloseqGraphTest.pdf |phyloseqGraphTest.html✨
phyloseqGraphTest/json (API)

# Install 'phyloseqGraphTest' in R:

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

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

On CRAN:

4.75 score 4 stars 14 scripts 634 downloads 2 mentions 3 exports 80 dependencies

Last updated 10 months agofrom:b12ebf799a. Checks:OK: 6 WARNING: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 01 2024
R-4.5-win	OK	Nov 01 2024
R-4.5-linux	WARNING	Nov 01 2024
R-4.4-win	OK	Nov 01 2024
R-4.4-mac	OK	Nov 01 2024
R-4.3-win	OK	Nov 01 2024
R-4.3-mac	OK	Nov 01 2024

Exports:graph_perm_test plot_permutations plot_test_network

Dependencies:ade4 ape askpass Biobase BiocGenerics biomformat Biostrings cli cluster coda codetools colorspace cpp11 crayon curl data.table digest fansi farver foreach generics GenomeInfoDb GenomeInfoDbData ggnetwork ggplot2 ggrepel glue gtable httr igraph IRanges isoband iterators jsonlite labeling lattice lifecycle magrittr MASS Matrix mgcv mime multtest munsell network nlme openssl permute phyloseq pillar pixmap pkgconfig plyr R6 RColorBrewer Rcpp RcppArmadillo reshape2 rhdf5 rhdf5filters Rhdf5lib rlang S4Vectors scales sna sp statnet.common stringi stringr survival sys tibble UCSC.utils utf8 vctrs vegan viridisLite withr XVector zlibbioc

Graph Testing Vignette

Julia Fukuyama

Rendered fromgt_vignette.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2018-03-13
Started: 2018-03-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
phyloseqGraphTest: Non-parametric graph-based testing for microbiome data.	phyloseqGraphTest-package
Performs graph-based permutation tests	graph_perm_test
Fortify method for networks of class 'igraph'	new_fortify.igraph
Plots the permutation distribution	plot_permutations
Plots the graph used for testing	plot_test_network
Print psgraphtest objects	print.psgraphtest
Rescale x to (0, 1), except if x is constant	scale_safely