https://github.com/scverse/mudata
Multimodal Data (.h5mu) implementation for Python
https://github.com/scverse/mudata
anndata data-analysis genomics mudata multi-omics multimodal-omics-analysis muon scverse
Last synced: 3 months ago
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Multimodal Data (.h5mu) implementation for Python
- Host: GitHub
- URL: https://github.com/scverse/mudata
- Owner: scverse
- License: bsd-3-clause
- Created: 2021-08-04T22:12:18.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2025-05-26T22:34:02.000Z (4 months ago)
- Last Synced: 2025-06-28T16:48:16.626Z (3 months ago)
- Topics: anndata, data-analysis, genomics, mudata, multi-omics, multimodal-omics-analysis, muon, scverse
- Language: Python
- Homepage: https://mudata.rtfd.io
- Size: 1.05 MB
- Stars: 99
- Watchers: 6
- Forks: 20
- Open Issues: 13
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
README
[](http://mudata.readthedocs.io/)
[](https://pypi.org/project/mudata)
[](https://scverse.org)
[](https://numfocus.org)
# MuData – multimodal data
[Documentation](https://mudata.readthedocs.io/) | [Publication](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02577-8)
For using `MuData` in multimodal omics applications see [`muon`](https://github.com/scverse/muon).
## Data structure
In the same vein as [AnnData](https://github.com/theislab/anndata) is designed to represent unimodal annotated datasets in Python, `MuData` is designed to provide functionality to load, process, and store multimodal omics data.
```
MuData
.obs -- annotation of observations (cells, samples)
.var -- annotation of features (genes, genomic loci, etc.)
.obsm -- multidimensional cell annotation,
incl. a boolean for each modality
that links .obs to the cells of that modality
.varm -- multidimensional feature annotation,
incl. a boolean vector for each modality
that links .var to the features of that modality
.mod
AnnData
.X -- data matrix (cells x features)
.obs -- cell metadata (assay-specific)
.var -- annotation of features (genes, peaks, genomic sites)
.obsm
.varm
.uns
.uns
```
## Overview
### Input
`MuData` can be thought of as a multimodal container, in which every modality is an AnnData object:
```py
from mudata import MuData
mdata = MuData({'rna': adata_rna, 'atac': adata_atac})
```
If multimodal data from 10X Genomics is to be read, convenient readers are provided by [`muon`](https://github.com/scverse/muon) that return a `MuData` object with AnnData objects inside, each corresponding to its own modality:
```py
import muon as mu
mu.read_10x_h5("filtered_feature_bc_matrix.h5")
# MuData object with n_obs × n_vars = 10000 × 80000
# 2 modalities
# rna: 10000 x 30000
# var: 'gene_ids', 'feature_types', 'genome', 'interval'
# atac: 10000 x 50000
# var: 'gene_ids', 'feature_types', 'genome', 'interval'
# uns: 'atac', 'files'
```
### I/O with `.h5mu` files
`MuData` objects represent modalities as collections of AnnData objects. These collections can be saved to disk and retrieved using HDF5-based `.h5mu` files, which design is based on `.h5ad` file structure.
```py
import mudata as md
mdata_pbmc.write("pbmc_10k.h5mu")
mdata = md.read("pbmc_10k.h5mu")
```
It allows to effectively use the hierarchical nature of HDF5 files and to read/write AnnData object directly from/to `.h5mu` files:
```py
adata = md.read("pbmc_10k.h5mu/rna")
md.write("pbmc_10k.h5mu/rna", adata)
```
## Citation
If you use `mudata` in your work, please cite the publication as follows:
> **MUON: multimodal omics analysis framework**
>
> Danila Bredikhin, Ilia Kats, Oliver Stegle
>
> _Genome Biology_ 2022 Feb 01. doi: [10.1186/s13059-021-02577-8](https://doi.org/10.1186/s13059-021-02577-8).
You can cite the scverse publication as follows:
> **The scverse project provides a computational ecosystem for single-cell omics data analysis**
>
> Isaac Virshup, Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso, Ilia Kats, Mikaela Koutrouli, Scverse Community, Bonnie Berger, Dana Pe’er, Aviv Regev, Sarah A. Teichmann, Francesca Finotello, F. Alexander Wolf, Nir Yosef, Oliver Stegle & Fabian J. Theis
>
> _Nat Biotechnol._ 2023 Apr 10. doi: [10.1038/s41587-023-01733-8](https://doi.org/10.1038/s41587-023-01733-8).
[//]: # (numfocus-fiscal-sponsor-attribution)
mudata is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).
If you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
