SpiecEasi
Sparse Inverse Covariance for Ecological Statistical Inference
Bioconductor version: 3.23 · Package version: 2.0.0
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 |
| Downloads rank | 133 |
| Source branch | RELEASE_3_23 |
| biocViews | GraphAndNetwork, Metagenomics, Microbiome, NetworkInference, Software |
Documentation
- Cross Domain SPIEC-EASI
- Introduction to SpiecEasi
- Learning latent variable graphical models
- pulsar: parallel utilities for model selection
- Troubleshooting
- Working with phyloseq
Download
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