# Loading the tidyomics ecosystem

## William Hutchison

### 2026-04-28

## Overview

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"               "plyranges"
    #  [5] "tidySpatialExperiment"    "tidyomics"

## The tidyomics ecosystem

### Core packages

The core packages are automatically loaded when you run `library(tidyomics)`:

Package | Intro | GitHub | Description
--- | --- | --- | ---
tidySummarizedExperiment | Vignette | GitHub | Tidy manipulation of SummarizedExperiment objects
tidySingleCellExperiment | Vignette | GitHub | Tidy manipulation of SingleCellExperiment objects
tidySeurat | Vignette | GitHub | Tidy manipulation of Seurat objects
tidySpatialExperiment | Vignette | GitHub | Tidy manipulation of SpatialExperiment objects
plyranges | Vignette | GitHub | Tidy manipulation of genomics ranges

### Additional manipulation packages

Package | Intro | GitHub | Description
--- | --- | --- | ---
plyinteractions | Vignette | GitHub | Tidy manipulation of genomic interactions

plyinteractions is under evaluation for inclusion in the core packages in future Bioconductor releases.

### Analysis packages

Package | Intro | GitHub | Description
--- | --- | --- | ---
tidybulk | Vignette | GitHub | Tidy bulk RNA-seq data analysis
nullranges | Vignette | GitHub | 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:

    BiocManager::install("tidyomics")

Additional packages can be installed independently as needed:

    # Additional manipulation package
    BiocManager::install("plyinteractions")

    # Analysis packages
    BiocManager::install("tidybulk")
    BiocManager::install("nullranges")

## Loading the tidyomics ecosystem

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.

Additional packages can be loaded independently as needed:

    # Additional manipulation package
    library(plyinteractions)

    # Analysis packages
    library(tidybulk)
    library(nullranges)

You are now ready to start using the tidyomics ecosystem.

    sessionInfo()
    #  R version 4.6.0 RC (2026-04-17 r89917)
    #  Platform: x86_64-pc-linux-gnu
    #  Running under: Ubuntu 24.04.4 LTS
    #
    #  Matrix products: default
    #  BLAS:   /home/biocbuild/bbs-3.24-bioc/R/lib/libRblas.so
    #  LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
    #
    #  locale:
    #   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
    #   [3] LC_TIME=en_GB              LC_COLLATE=C
    #   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
    #   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
    #   [9] LC_ADDRESS=C               LC_TELEPHONE=C
    #  [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
    #
    #  time zone: America/New_York
    #  tzcode source: system (glibc)
    #
    #  attached base packages:
    #  [1] stats     graphics  grDevices utils     datasets  methods   base
    #
    #  loaded via a namespace (and not attached):
    #   [1] compiler_4.6.0  magrittr_2.0.5  cli_3.6.6       tools_4.6.0
    #   [5] otel_0.2.0      glue_1.8.1      tidyomics_1.9.0 vctrs_0.7.3
    #   [9] stringi_1.8.7   knitr_1.51      stringr_1.6.0   xfun_0.57
    #  [13] lifecycle_1.0.5 rlang_1.2.0     evaluate_1.0.5  purrr_1.2.2