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SpiecEasi
This is thedevelopment version of SpiecEasi; to use it, please install thedevel version of Bioconductor.
Sparse Inverse Covariance for Ecological Statistical Inference
Bioconductor version: Development (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 (from within R, enter
citation("SpiecEasi")):Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")# The following initializes usage of Bioc develBiocManager::install(version='devel')BiocManager::install("SpiecEasi")For older versions of R, please refer to the appropriateBioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | GraphAndNetwork,Metagenomics,Microbiome,NetworkInference,Software |
| Version | 1.99.3 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | GPL (>= 3) |
| Depends | R (>= 4.4.0) |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | SpiecEasi_1.99.3.zip |
| macOS Binary (x86_64) | SpiecEasi_1.99.3.tgz |
| macOS Binary (arm64) | SpiecEasi_1.99.3.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 |