anansi

This is the development version of anansi; to use it, please install the devel version of Bioconductor.

Annotation-Based Analysis of Specific Interactions

Bioconductor version: Development (3.22)

Studies including both microbiome and metabolomics data are becoming more common. Often, it would be helpful to integrate both datasets in order to see if they corroborate each others patterns. All vs all association is imprecise and likely to yield spurious associations. This package takes a knowledge-based approach to constrain association search space, only considering metabolite-function pairs that have been recorded in a pathway database. This package also provides a framework to assess differential association.

Author: Thomaz Bastiaanssen [aut, cre] ORCID: 0000-0001-6891-734X , Thomas Quinn [aut] ORCID: 0000-0003-0286-6329 , Giulio Benedetti [aut] ORCID: 0000-0002-8732-7692 , Tuomas Borman [aut] ORCID: 0000-0002-8563-8884 , Leo Lahti [aut] ORCID: 0000-0001-5537-637X

Maintainer: Thomaz Bastiaanssen <thomazbastiaanssen at gmail.com>

Citation (from within R, enter citation("anansi")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("anansi")

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("anansi")

1. Getting started with anansi	HTML	R Script
2. Working with (bi)adjacency matrices	HTML	R Script
3. Differential associations	HTML	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	KEGG, Metabolomics, Microbiome, Pathways, Regression, Software
Version	0.99.4
In Bioconductor since	BioC 3.22 (R-4.5)
License	GPL-3
Depends	R (>= 4.5.0)
Imports	S7, stats, methods, igraph, Matrix, forcats, S4Vectors, SummarizedExperiment, MultiAssayExperiment, SingleCellExperiment, TreeSummarizedExperiment, rlang, ggplot2, ggforce, patchwork, ggraph, tidygraph
System Requirements
URL	https://github.com/thomazbastiaanssen/anansi https://thomazbastiaanssen.github.io/anansi
Bug Reports	https://github.com/thomazbastiaanssen/anansi/issues

Suggests	BiocStyle, dplyr, tidyr, graph, mia, KEGGREST, testthat (>= 3.0.0), knitr, rmarkdown
Linking To
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	anansi_0.99.4.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)	anansi_0.99.4.tgz
macOS Binary (arm64)	anansi_0.99.4.tgz
Source Repository	git clone https://git.bioconductor.org/packages/anansi
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/anansi
Bioc Package Browser	https://code.bioconductor.org/browse/anansi/
Package Short Url	https://bioconductor.org/packages/anansi/
Package Downloads Report	Download Stats