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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/strainspy/ |
| Package Short Url | https://bioconductor.org/packages/strainspy/ |
| Package Downloads Report | Download Stats |