Package: microbiomeDASim 1.21.0

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_1.21.0.tar.gz
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microbiomeDASim.pdf |microbiomeDASim.html✨
microbiomeDASim/json (API)
NEWS

# 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-1.19.0(bioc 3.20)microbiomeDASim-1.18.0(bioc 3.19)

microbiome visualization software

4.48 score 3 stars 1 scripts 172 downloads 1 mentions 9 exports 93 dependencies

Last updated 23 days agofrom:a5f0a435a4. Checks:OK: 5 NOTE: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	NOTE	Oct 31 2024
R-4.5-linux	NOTE	Oct 30 2024
R-4.4-win	OK	Oct 31 2024
R-4.4-mac	OK	Oct 31 2024
R-4.3-win	OK	Oct 31 2024
R-4.3-mac	OK	Oct 31 2024

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 askpass Biobase BiocGenerics biomformat Biostrings bitops caTools cli cluster codetools colorspace cpp11 crayon curl data.table digest fansi farver foreach GenomeInfoDb GenomeInfoDbData ggplot2 glmnet glue gmm gplots gtable gtools httr igraph IRanges isoband iterators jsonlite KernSmooth labeling lattice lifecycle limma locfit magrittr MASS Matrix matrixStats metagenomeSeq mgcv mime multtest munsell mvtnorm nlme openssl pbapply permute phyloseq pillar pixmap pkgconfig plyr R6 RColorBrewer Rcpp RcppArmadillo RcppEigen reshape2 rhdf5 rhdf5filters Rhdf5lib rlang S4Vectors sandwich scales shape sp statmod stringi stringr survival sys tibble tmvtnorm UCSC.utils utf8 vctrs vegan viridisLite withr Wrench XVector zlibbioc zoo

microbiomeDASim

Rendered frommicrobiomeDASim.Rnwusingknitr::knitron Oct 30 2024.

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