MUDAN

<img src="docs/assets/img/logo.png" width=128px>

Multi-sample Unified Discriminant ANalysis

(Fun fact: mudan 牡丹 means peony in Chinese)

Please note that MUDAN is still in active development and will likely see substantial changes in terms of its algorithms, data structure, and otherwise general functionalities in ways that may not be backwards compatible.

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Motivation

To analyze multiple single-cell RNA-seq samples in a coherent manner in order to acheive joint annotation of cell types across patients, time-points, and batches.

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Benefits and Capabilities

Enhanced visualizations

• Detected clusters are artificially separated for visualization purposes only

<img src="docs/assets/img/visualization.png" width=500px>

Fast subpopulation detection and characterization

• Graph-based community detection to identify subpopulations
• Stability analysis to ensure transcriptionally distinct subpopulations
• Differential gene expression and marker selection functionalities

<img src="docs/assets/img/stability.png" width=500px> <img src="docs/assets/img/diffexp.png" width=500px>

Multi-sample clustering

• Preserves variation observed in each sample
• Ideal for when samples may differ in cell type composition

<img src="docs/assets/img/batch.png" width=500px>

Please see the vignettes for more information

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Install

require(devtools)
devtools::install_github("JEFworks/MUDAN")

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Contributing

I welcome any bug reports, enhancement requests, and other contributions. To submit a bug report or enhancement request, please use the MUDAN GitHub issues tracker. For more substantial contributions, please fork this repo, push your changes to your fork, and submit a pull request with a good commit message.