https://github.com/scverse/muon-tutorials
Tutorials for multimodal omics data analysis
https://github.com/scverse/muon-tutorials
mudata multi-omics muon scverse single-cell
Last synced: 3 months ago
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Tutorials for multimodal omics data analysis
- Host: GitHub
- URL: https://github.com/scverse/muon-tutorials
- Owner: scverse
- License: bsd-3-clause
- Created: 2020-09-11T15:37:03.000Z (about 5 years ago)
- Default Branch: master
- Last Pushed: 2025-02-28T16:20:18.000Z (7 months ago)
- Last Synced: 2025-02-28T21:13:21.248Z (7 months ago)
- Topics: mudata, multi-omics, muon, scverse, single-cell
- Language: Jupyter Notebook
- Homepage: https://muon-tutorials.rtfd.io/
- Size: 17.7 MB
- Stars: 13
- Watchers: 11
- Forks: 7
- Open Issues: 6
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Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Tutorials for multimodal omics data analysis
This repository contains examples showcasing processing and interpretation of multimodal omics data using [muon](https://github.com/scverse/muon).
## Single-cell ATAC and gene expression
- [These tutorials on 10k PBMC cells](single-cell-rna-atac/pbmc10k) demonstrate how to work with chromatin accessibility and gene expression data from individual cells.
## CITE-seq
- [This tutorial on 5k PBMC cells](cite-seq/1-CITE-seq-PBMC-5k.ipynb) describes how to process CITE-seq data (including antibody-derived tags counts normalisation) and how to integrate surface protein abundance and gene expression.
## Spatiotemporal omics
- [These tutorials](mefisto/) show how smooth factors can be learnt, across time and space, with models such as [MEFISTO](https://biofam.github.io/MOFA2/MEFISTO).
## Biomedical applications
- [Chronic lymphocytic leukemia (CLL) notebook](CLL.ipynb) gives a glimpse of the utility of multi-omics data integration in biomedical applications.
# Other resources
For the list of software packages, you might find useful the [awesome multi-omics](https://github.com/mikelove/awesome-multi-omics) repository.
[//]: # (numfocus-fiscal-sponsor-attribution)
muon 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.
