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Knowledge-based multi-modal integration using anansi The anansi hex sticker

Introduction

The anansi package computes and compares the association between the features of two ’omics data sets that are known to interact based on a database such as KEGG. Studies including both microbiome and metabolomics data are becoming more common. Often, it would be helpful to integrate both data sets 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 interactions that have been recorded in a pathway database. This package also provides a framework to assess differential association.

While anansi is geared towards metabolite-function interactions in the context of host-microbe interactions, it is perfectly capable of handling any other pair of data sets where some features interact canonically.

Installation instructions

Get the latest stable R release from CRAN. Then install anansi from Bioconductor using the following code:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("anansi")

And the development version from GitHub with remotes:

install.packages("remotes")
remotes::install_github("thomazbastiaanssen/anansi")

Getting started using anansi

See the vignettes on the package site. Additionally, a preprint is available.

Citation

Below is the citation output from using citation('anansi') in R.

print(citation("anansi"), bibtex = TRUE)
#> To cite anansi in publications use:
#> 
#>   Bastiaanssen TFS, Quinn TP, Cryan JF (2023) Knowledge-based
#>   Integration of Multi-Omic Datasets with Anansi: Annotation-based
#>   Analysis of Specific Interactions arXiv. doi:
#>   10.48550/arXiv.2305.10832
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     title = {Knowledge-based Integration of Multi-Omic Datasets with Anansi: Annotation-based Analysis of Specific Interactions},
#>     author = {Thomaz F S Bastiaanssen and Thomas P Quinn and John F Cryan},
#>     journal = {arXiv},
#>     year = {2023},
#>     doi = {10.48550/arXiv.2305.10832},
#>   }

Code of Conduct

Please note that the anansi project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.