SpiecEasi
This is the development version of SpiecEasi; for the stable release version, see SpiecEasi.
All Bioconductor versions of SpiecEasi
3.24 (devel), 3.23 (release)
Sparse Inverse Covariance for Ecological Statistical Inference
Bioconductor version: 3.24 · Package version: 2.1.1
Estimate networks from the precision matrix of compositional microbial abundance data.
Author: Zachary Kurtz [aut, cre], Christian Mueller [aut], Emily Miraldi [aut], Richard Bonneau [aut], Laura Tipton [ctb]
Maintainer: Zachary Kurtz <zdkurtz at gmail.com>
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 2.1.1, https://bioconductor.org/packages/SpiecEasi.
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("SpiecEasi")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 2.1.1 |
| License | GPL (>= 3) |
| URL | https://github.com/zdk123/SpiecEasi |
| Bug Reports | https://github.com/zdk123/SpiecEasi/issues |
| Last updated | 2026-04-29 |
| In Bioconductor since | BioC 3.23 (R-4.6) (less than a year) |
| Downloads rank | 2051 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | GraphAndNetwork, Metagenomics, Microbiome, NetworkInference, Software |
| Package Short Url | https://bioconductor.org/packages/SpiecEasi/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SpiecEasi")| Cross Domain SPIEC-EASI | HTML | R Script |
| Introduction to SpiecEasi | HTML | R Script |
| Learning latent variable graphical models | HTML | R Script |
| pulsar: parallel utilities for model selection | HTML | R Script |
| Troubleshooting | HTML | R Script |
| Working with phyloseq | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | SpiecEasi_2.1.1.tar.gz |
| Windows binary (x86_64) | SpiecEasi_2.1.1.zip |
| macOS binary (arm64) | SpiecEasi_2.1.1.tgz |
| macOS binary (x86_64) | SpiecEasi_2.1.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SpiecEasi |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SpiecEasi |
| Package Downloads Report | Download Stats |
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