strainspy
This is the development version of strainspy; to use it, please install the devel version of Bioconductor.
Strain Level Microbiome Wide Association Studies
Bioconductor version: Development (3.24)
Fits statistical models to detect microbial strains associated with a phenotype. For small sample sizes, models can be fitted using empirical Bayes maximum a posteriori (MAP) priors to improve detection power. Supports various experimental design scenarios, including repeated measures.
Author: Gerry Tonkin-Hill [aut], Sudaraka Mallawaarachchi [aut, cre] 
Maintainer: Sudaraka Mallawaarachchi <smallawaarachchi at gmail.com>
citation("strainspy")):Gerry Tonkin-Hill, Sudaraka Mallawaarachchi. strainspy: Strain Level Microbiome Wide Association Studies. doi:10.18129/B9.bioc.strainspy, R package version 0.99.3, https://bioconductor.org/packages/strainspy.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("strainspy")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("strainspy")| strainspy Workflow | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, ExperimentalDesign, Metagenomics, MicrobialStrain, Microbiome, Regression, Sequencing, Software |
| Version | 0.99.3 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.1.0) |
| Imports | ape, BiocParallel, data.table, dplyr, ggforce, ggplot2, ggrepel, ggthemes, ggtree, glmmTMB, graphics, grDevices, harmonicmeanp, lmerTest, magrittr, Matrix, methods, patchwork, purrr, R.utils (>= 2.13.0), S4Vectors, stats, stringr, SummarizedExperiment, rlang, tibble, tidyr, tools, utils, viridis |
| System Requirements | |
| URL | https://github.com/gtonkinhill/strainspy https://sudaraka88.r-universe.dev/strainspy |
| Bug Reports | https://github.com/gtonkinhill/strainspy/issues |
See More
| Suggests | betareg, BiocStyle, compositions, fastglm, future, gamlss, gamlss.dist, knitr, mgcv, rmarkdown, testthat (>= 3.0.0), vegan, emmeans |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | strainspy_0.99.3.tar.gz |
| Windows Binary (x86_64) | strainspy_0.99.3.zip |
| macOS Binary (big-sur-x86_64) | strainspy_0.99.3.tgz |
| macOS Binary (sonoma-arm64) | strainspy_0.99.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/strainspy |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/strainspy |
| Package Short Url | https://bioconductor.org/packages/strainspy/ |
| Package Downloads Report | Download Stats |