<!-- README.md is generated from README.Rmd. Please edit that file -->
## 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.
