# MuDataSeurat

**Repository Path**: joyeric_admin_admin/MuDataSeurat

## Basic Information

- **Project Name**: MuDataSeurat
- **Description**: https://github.com/PMBio/MuDataSeurat.git
- **Primary Language**: Unknown
- **License**: MulanPSL-2.0
- **Default Branch**: main
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2024-06-15
- **Last Updated**: 2024-06-15

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# MuDataSeurat

[![R-CMD-check](https://github.com/PMBio/MuDataSeurat/workflows/R-CMD-check/badge.svg)](https://github.com/PMBio/MuDataSeurat/actions) [![pkgdown](https://github.com/PMBio/MuDataSeurat/workflows/pkgdown/badge.svg)](https://github.com/PMBio/MuDataSeurat/actions)

[Documentation](https://pmbio.github.io/MuDataSeurat/) | [Preprint](https://www.biorxiv.org/content/10.1101/2021.06.01.445670v1) | [Discord](https://discord.com/invite/MMsgDhnSwQ)

`MuDataSeurat` is a package that provides I/O functionality for `.h5mu` files and [Seurat](https://satijalab.org/seurat/) objects.

You can learn more about multimodal data containers in the [`mudata` documentation](https://mudata.readthedocs.io/en/latest/io/mudata.html).

## Installation

```R
remotes::install_github("pmbio/MuDataSeurat")
```

## Quick start

`MuDataSeurat` provides a set of I/O operations for multimodal data.

`MuDataSeurat` implements `WriteH5MU()` that saves Seurat objects to `.h5mu` files that can be further integrated into workflows in multiple programming languages, including the [`muon` Python library](https://github.com/pmbio/muon) and the [`Muon.jl` Julia library](https://github.com/pmbio/Muon.jl). `ReadH5MU()` reads `.h5mu` files into Seurat objects. 

`MuDataSeurat` currently works for Seurat objects of v3 and above.

### Writing files

Start with an existing dataset, e.g. a [Seurat](https://github.com/satijalab/seurat) object with CITE-seq data:

```R
library(SeuratData)
InstallData("bmcite")
bm <- LoadData(ds = "bmcite")
```

`WriteH5MU()` allows to save the object into a `.h5mu` file:

```R
library(MuDataSeurat)
WriteH5MU(bm, "bmcite.h5mu")
```

Please note that only standardised parts of the object are written to the file, and extra information from specific methods, stored in the Seurat object, might be omitted upon writing the file.

### Reading files

```R
bm <- ReadH5MU("bmcite.h5mu")
```

Please note that only the intersection of cells is currently loaded into the Seurat object due to the object structure limitation. Multimodal embeddings (global `.obsm` slot) are loaded with the `assay.used` field set to the default assay. Embeddings names are changed in order to comply with R & Seurat requirements and conventions.

## Relevant projects

Other R packages for multimodal I/O include:

- [MuData](https://github.com/PMBio/MuDataMAE) for [MultiAssayExperiment](https://bioconductor.org/packages/release/bioc/html/MultiAssayExperiment.html) objects
- [SeuratDisk](https://github.com/mojaveazure/seurat-disk)