https://github.com/scverse/muon.jl
Muon for Julia
https://github.com/scverse/muon.jl
anndata julia mudata multi-omics muon omics scverse single-cell
Last synced: 3 months ago
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Muon for Julia
- Host: GitHub
- URL: https://github.com/scverse/muon.jl
- Owner: scverse
- License: bsd-3-clause
- Created: 2021-03-05T12:38:48.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2025-05-20T09:18:16.000Z (5 months ago)
- Last Synced: 2025-07-07T01:08:58.293Z (3 months ago)
- Topics: anndata, julia, mudata, multi-omics, muon, omics, scverse, single-cell
- Language: Julia
- Homepage: https://scverse.github.io/Muon.jl/dev
- Size: 1.08 MB
- Stars: 28
- Watchers: 3
- Forks: 6
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.cff
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README
# Muon for Julia
[](https://scverse.github.io/Muon.jl/dev)
Muon is originally [a Python library to work with multimodal data](https://github.com/scverse/muon). `Muon.jl` brings the ability to work with the same data structures to Julia.
`Muon.jl` implements I/O for `.h5mu` and `.h5ad` files as well as basic operations on the multimodal objects.
## Introduction
Datasets can usually be represented as matrices with values for the _variables_ measured in different samples, or _observations_. Variables and observations tend to have annotations attached to them, a typical example would be metadata annotating samples. Such a dataset with the matrix in its centre and different kinds of annotations associated with it can be stored conveniently in an [annotated data](https://anndata.readthedocs.io/en/latest/) object, `AnnData` for short.
Multimodal datasets are characterised by the variables coming from different generative processes. Each of these _modalities_ is an annotated dataset by itself, but they can be managed and analyzed together within a `MuData` object.
## Examples
`MuData` objects can be created from `.h5mu` files:
```julia
using Muon
mdata = readh5mu("pbmc10k.h5mu");
```
Individual modalities can be accessed directly by their name:
```julia
mdata["rna"]
# => AnnData object 10110 ✕ 101001
```
Low-dimensional representations of the data can be plotted with the plotting library of choice:
```julia
using DataFrames
using GLMakie
using AlgebraOfGraphics
df = DataFrame(LF1 = mdata.obsm["X_umap"][1,:],
LF2 = mdata.obsm["X_umap"][2,:]);
data(df) * mapping(:LF1, :LF2) * visual(Scatter) |> draw
```
[//]: # (numfocus-fiscal-sponsor-attribution)
Muon.jl 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.
