## Overview The \[tidyomics\](https://github.com/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 \[tidyverse\](https://www.tidyverse.org/) 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: \`\`\` r tidyomics\_packages() \`\`\` # \[1\] "tidySummarizedExperiment" "tidySingleCellExperiment" # \[3\] "tidyseurat" "tidybulk" # \[5\] "plyranges" "nullranges" # \[7\] "purrr" "rlang" # \[9\] "stringr" "cli" # \[11\] "utils" "tidyomics" ## The tidyomics ecosystem You can find out more about each package in the tidyomics ecosystem here: | Package | Intro | GitHub | Description | |-------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------|----------------------------------------------------------------------|---------------------------------------------------| | \[tidybulk\](https://stemangiola.github.io/tidybulk/) | \[Vignette\](https://stemangiola.github.io/tidybulk/articles/introduction.html) | \[GitHub\](https://github.com/stemangiola/tidybulk/) | Tidy bulk RNA-seq data analysis | | \[tidySummarizedExperiment\](https://stemangiola.github.io/tidySummarizedExperiment/) | \[Vignette\](https://stemangiola.github.io/tidySummarizedExperiment/articles/introduction.html) | \[GitHub\](https://github.com/stemangiola/tidySummarizedExperiment) | Tidy manipulation of SummarizedExperiment objects | | \[tidySingleCellExperiment\](https://stemangiola.github.io/tidySingleCellExperiment) | \[Vignette\](https://stemangiola.github.io/tidySingleCellExperiment/articles/introduction.html) | \[GitHub\](https://github.com/stemangiola/tidySingleCellExperiment) | Tidy manipulation of SingleCellExperiment objects | | \[tidySeurat\](https://stemangiola.github.io/tidyseurat/) | \[Vignette\](https://stemangiola.github.io/tidyseurat/articles/introduction.html) | \[GitHub\](https://github.com/stemangiola/tidyseurat) | Tidy manipulation of Seurat objects | | \[tidySpatialExperiment\](https://william-hutchison.github.io/tidySpatialExperiment/) | \[Vignette\](https://william-hutchison.github.io/tidySpatialExperiment/articles/overview.html) | \[GitHub\](https://github.com/william-hutchison/tidySpatialExperiment) | Tidy manipulation of SpatialExperiment objects | | \[plyranges\](https://sa-lee.github.io/plyranges/) | \[Vignette\](https://sa-lee.github.io/plyranges/articles/an-introduction.html) | \[GitHub\](https://github.com/sa-lee/plyranges) | Tidy manipulation of genomics ranges | | \[plyinteractions\](https://tidyomics.github.io/plyinteractions/) | \[Vignette\](https://tidyomics.github.io/plyinteractions/articles/plyinteractions.html) | \[GitHub\](https://github.com/tidyomics/plyinteractions) | Tidy manipulation of genomic interactions | | \[nullranges\](https://nullranges.github.io/nullranges/) | \[Vignette\](https://nullranges.github.io/nullranges/articles/nullranges.html) | \[GitHub\](https://github.com/nullranges/nullranges/) | Generation of null genomic range sets | ## Installation Installing the \*\*tidyomics\*\* package will install all core packages of the \*tidyomics\* ecosystem. The \*\*tidyomics\*\* package can be installed from Bioconductor: \`\`\` r 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: \`\`\` r BiocManager::install("plyinteractions") BiocManager::install("tidySpatialExperiment") \`\`\` ## Loading the \*tidyomics\* ecosystem The core \*tidyomics\* packages can be attached with: \`\`\` r 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: \`\`\` r library(plyinteractions) library(tidySpatialExperiment) \`\`\` You are now ready to start using the \*tidyomics\* ecosystem.