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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:

tidyomics_packages()

#   [1] "tidySummarizedExperiment" "tidySingleCellExperiment"
#   [3] "tidyseurat"               "tidybulk"                
#   [5] "plyranges"                "nullranges"              
#   [7] "purrr"                    "rlang"                   
#   [9] "stringr"                  "cli"                     
#  [11] "utils"                    "tidyomics"

You can find out more about each package in the tidyomics ecosystem here:

Installing the tidyomics package will install all core packages of the tidyomics ecosystem. The tidyomics package can be installed from Bioconductor:

BiocManager::install("tidyomics")

plyinteractions and tidySpatialExperiment are two new packages in the tidyomics ecosystem. plyinteractions and tidySpatialExperiment are both ready to use and are available in Bioconductor. The packages are now reaching maturity and will be added to the core packages for automatic installation mid-2024.

For the time being, plyinteractions and tidySpatialExperiment can be installed independently:

BiocManager::install("plyinteractions")
BiocManager::install("tidySpatialExperiment")

The core tidyomics packages can be attached 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 and tidySpatialExperiment can be loaded independently:

library(plyinteractions)
library(tidySpatialExperiment)

You are now ready to start using the tidyomics ecosystem.