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")):
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")
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 |
| 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 |
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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/SpiecEasi/ |
| Package Short Url | https://bioconductor.org/packages/SpiecEasi/ |
| Package Downloads Report | Download Stats |