Tidyomics

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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"

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.

You are now ready to start using the tidyomics ecosystem.