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:
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-4.5-any)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
Last updated 1 years agofrom:b12ebf799a. Checks:8 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 30 2025 |
| R-4.5-win | OK | Jan 30 2025 |
| R-4.5-mac | OK | Jan 30 2025 |
| R-4.5-linux | OK | Jan 30 2025 |
| R-4.4-win | OK | Jan 30 2025 |
| R-4.4-mac | OK | Jan 30 2025 |
| R-4.3-win | OK | Dec 01 2024 |
| R-4.3-mac | OK | Dec 31 2024 |
Exports:graph_perm_testplot_permutationsplot_test_network
Dependencies:ade4apeaskpassBiobaseBiocGenericsbiomformatBiostringscliclustercodacodetoolscolorspacecpp11crayoncurldata.tabledigestfansifarverforeachgenericsGenomeInfoDbGenomeInfoDbDataggnetworkggplot2ggrepelgluegtablehttrigraphIRangesisobanditeratorsjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemulttestmunsellnetworknlmeopensslpermutephyloseqpillarpixmappkgconfigplyrR6RColorBrewerRcppRcppArmadilloreshape2rhdf5rhdf5filtersRhdf5librlangS4Vectorsscalessnaspstatnet.commonstringistringrsurvivalsystibbleUCSC.utilsutf8vctrsveganviridisLitewithrXVector
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 |
