Package: microbiomeDASim 1.27.0

Justin Williams

microbiomeDASim: Microbiome Differential Abundance Simulation

A toolkit for simulating differential microbiome data designed for longitudinal analyses. Several functional forms may be specified for the mean trend. Observations are drawn from a multivariate normal model. The objective of this package is to be able to simulate data in order to accurately compare different longitudinal methods for differential abundance.

Authors:Justin Williams, Hector Corrada Bravo, Jennifer Tom, Joseph Nathaniel Paulson

microbiomeDASim_1.27.0.tar.gz
microbiomeDASim_1.27.0.zip(r-4.7)microbiomeDASim_1.27.0.zip(r-4.6)microbiomeDASim_1.27.0.zip(r-4.5)
microbiomeDASim_1.27.0.tgz(r-4.6-any)microbiomeDASim_1.27.0.tgz(r-4.5-any)
microbiomeDASim_1.27.0.tar.gz(r-4.7-any)microbiomeDASim_1.27.0.tar.gz(r-4.6-any)
microbiomeDASim_1.27.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
microbiomeDASim/json (API)

# Install 'microbiomeDASim' in R:

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

Bug tracker:https://github.com/williazo/microbiomedasim/issues

On BioConductor:microbiomeDASim-1.27.0(bioc 3.24)microbiomeDASim-1.26.0(bioc 3.23)

microbiome visualization software

4.48 score 3 stars 6 scripts 333 downloads 1 mentions 9 exports 77 dependencies

Last updated from:aefd984661. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	205
linux-devel-x86_64	NOTE	378
source / vignettes	OK	302
linux-release-x86_64	NOTE	364
macos-release-arm64	NOTE	169
macos-oldrel-arm64	NOTE	184
windows-devel	NOTE	229
windows-release	NOTE	244
windows-oldrel	NOTE	223
wasm-release	OK	166

Exports:gen_norm_microbiome gen_norm_microbiome_obs ggplot_spaghetti mean_trend mvrnorm_corr_gen mvrnorm_sim mvrnorm_sim_obs simulate2MRexperiment simulate2phyloseq

Dependencies:ade4 ape Biobase BiocGenerics biomformat Biostrings bitops caTools cli cluster codetools cpp11 crayon data.table digest farver foreach generics ggplot2 glmnet glue gmm gplots gtable gtools igraph IRanges isoband iterators jsonlite KernSmooth labeling lattice lifecycle limma locfit magrittr MASS Matrix matrixStats metagenomeSeq mgcv multtest mvtnorm nlme pbapply permute phyloseq pixmap pkgconfig plyr R6 RColorBrewer Rcpp RcppArmadillo RcppEigen reshape2 rlang S4Vectors S7 sandwich scales Seqinfo shape sp statmod stringi stringr survival tmvtnorm vctrs vegan viridisLite withr Wrench XVector zoo

microbiomeDASim

Introduction | Installation | Motivation | Statistical Methodology | Session Info

Rendered frommicrobiomeDASim.Rnwusingknitr::knitr

Last update: 2020-01-15
Started: 2019-08-26

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Beta Specification Check	form_beta_check
Generate Longitduinal Differential Abundance from Multivariate Normal	gen_norm_microbiome
Generate Longitduinal Differential Abundance from Multivariate Normal with Observed Data	gen_norm_microbiome_obs
Spaghetti Plots using 'ggplot2'	ggplot_spaghetti
Function for Generating Various Longitudinal Mean Trends	mean_trend
Generate Multivariate Random Normal Longitudinal Data	mvrnorm_corr_gen
Simulate Microbiome Longitudinal Data from Multivariate Random Normal	mvrnorm_sim
Simulate Microbiome Longitudinal Data from Multivariate Random Normal with Observed Data	mvrnorm_sim_obs
Convert simulated output to MRexperiment object	simulate2MRexperiment
Convert simulated output to phyloseq object	simulate2phyloseq