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-4.7-any)phyloseqGraphTest_0.1.1.zip(r-4.6-any)phyloseqGraphTest_0.1.1.zip(r-4.5-any)
phyloseqGraphTest_0.1.1.tgz(r-4.6-any)phyloseqGraphTest_0.1.1.tgz(r-4.5-any)
phyloseqGraphTest_0.1.1.tar.gz(r-4.7-any)phyloseqGraphTest_0.1.1.tar.gz(r-4.6-any)
phyloseqGraphTest_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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:

4.86 score 4 stars 18 scripts 482 downloads 2 mentions 3 exports 66 dependencies

Last updated from:b12ebf799a. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	235
source / vignettes	OK	242
linux-release	OK	250
macos-release	OK	237
macos-oldrel	OK	235
windows-devel	OK	170
windows-release	OK	153
windows-oldrel	OK	161
wasm-release	OK	130

Exports:graph_perm_test plot_permutations plot_test_network

Dependencies:ade4 ape Biobase BiocGenerics biomformat Biostrings cli cluster coda codetools cpp11 crayon data.table digest farver foreach generics ggnetwork ggplot2 ggrepel glue gtable igraph IRanges isoband iterators jsonlite labeling lattice lifecycle magrittr MASS Matrix mgcv multtest network nlme permute phyloseq pillar pixmap pkgconfig plyr R6 RColorBrewer Rcpp RcppArmadillo reshape2 rlang S4Vectors S7 scales Seqinfo sna sp statnet.common stringi stringr survival tibble utf8 vctrs vegan viridisLite withr XVector

Graph Testing Vignette

Rendered fromgt_vignette.Rmdusingknitr::rmarkdown

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