The tidyomics ecosystem is a set of packages for omics data analysis that work together in harmony; they share common Bioconductor data representations and API design consistent with the tidyverse ecosystem. The tidyomics package is designed to make it easy to install and load core packages from the tidyomics ecosystem with a single command.
The core packages are:
The tidyomics package can be installed from GitHub:
remotes::install_github("tidyomics/tidyomics")
The plyinteractions, tidySpatialExperiment and tidytof packages are not yet available for automatic installation. For the time being, plyinteractions and tidySpatialExperiment can be installed independently:
BiocManager::install("tidyomics/plyinteractions")
BiocManager::install("william-hutchison/tidySpatialExperiment")
And tidytof can be installed via GitHub.
The core tidyomics packages and supporting tidyverse packages can be loaded with:
library(tidyomics)
This command also produces a summary of package versions and function conflicts. Function conflicts are a point of ongoing development and will be addressed over time.
plyinteractions, tidySpatialExperiment and tidytof can be loaded independently:
library(plyinteractions)
library(tidySpatialExperiment)
library(tidytof)
You are now ready to start using the tidyomics ecosystem.