SpiecEasi
Sparse Inverse Covariance for Ecological Statistical Inference
Bioconductor version: 3.23 · Package version: 2.0.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Estimate networks from the precision matrix of compositional microbial abundance data.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SpiecEasi")Details
| Maintainer | Zachary Kurtz <zdkurtz@gmail.com> |
| Author | Zachary Kurtz [aut, cre], Christian Mueller [aut], Emily Miraldi [aut], Richard Bonneau [aut], Laura Tipton [ctb] |
| License | GPL (>= 3) |
| URL | https://github.com/zdk123/SpiecEasi |
| Bug Reports | https://github.com/zdk123/SpiecEasi/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | GraphAndNetwork, Metagenomics, Microbiome, NetworkInference, Software |
| Package Short Url | https://bioconductor.org/packages/SpiecEasi/ |
Citation
From within R, enter citation("SpiecEasi"):
Zachary Kurtz, Christian Mueller, Emily Miraldi, Richard Bonneau. SpiecEasi: Sparse Inverse Covariance for Ecological Statistical Inference. doi:10.18129/B9.bioc.SpiecEasi, R package version 2.0.0, https://bioconductor.org/packages/SpiecEasi.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- Cross Domain SPIEC-EASI
- Introduction to SpiecEasi
- Learning latent variable graphical models
- pulsar: parallel utilities for model selection
- Troubleshooting
- Working with phyloseq
Download
Follow the installation instructions to use this package in your R session.
| Source package | SpiecEasi_2.0.0.tar.gz |
| Windows binary (x86_64) | SpiecEasi_2.0.0.zip |
| macOS binary (arm64) | SpiecEasi_2.0.0.tgz |
| macOS binary (x86_64) | SpiecEasi_2.0.0.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: stats, methods, graphics, grDevices, huge (>= 1.3.2), pulsar (>= 0.3.11), MASS, VGAM, Matrix (>= 1.5), glmnet, phyloseq
LinkingTo: Rcpp, RcppArmadillo
Suggests: parallel, boot, igraph, batchtools, testthat, covr, knitr, BiocStyle, rmarkdown, RefManageR, sessioninfo, magick