SpiecEasi
This is the released version of SpiecEasi; for the devel version, see SpiecEasi.
Sparse Inverse Covariance for Ecological Statistical Inference
Bioconductor version: Release (3.23)
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("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.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SpiecEasi")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("SpiecEasi")| Cross Domain SPIEC-EASI | HTML | R Script |
| Learning latent variable graphical models | HTML | R Script |
| Working with phyloseq | HTML | R Script |
| pulsar: parallel utilities for model selection | HTML | R Script |
| Introduction to SpiecEasi | HTML | R Script |
| Troubleshooting | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GraphAndNetwork, Metagenomics, Microbiome, NetworkInference, Software |
| Version | 2.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | GPL (>= 3) |
| 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 |
| System Requirements | |
| URL | https://github.com/zdk123/SpiecEasi |
| Bug Reports | https://github.com/zdk123/SpiecEasi/issues |
See More
| Suggests | parallel, boot, igraph, batchtools, testthat, covr, knitr, BiocStyle, rmarkdown, RefManageR, sessioninfo, magick |
| Linking To | Rcpp, RcppArmadillo |
| 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 | SpiecEasi_2.0.0.tar.gz |
| Windows Binary (x86_64) | SpiecEasi_2.0.0.zip |
| macOS Binary (big-sur-x86_64) | SpiecEasi_2.0.0.tgz |
| macOS Binary (sonoma-arm64) | SpiecEasi_2.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SpiecEasi |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SpiecEasi |
| Package Short Url | https://bioconductor.org/packages/SpiecEasi/ |
| Package Downloads Report | Download Stats |