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# MultiMAP |
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# MultiMAP
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**MultiMAP** is a method for integrating single cell multi-omics. MultiMAP can also be used for batch correction. More detail is available in our [paper](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02565-y). |
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**MultiMAP** is a method for integrating single cell multi-omics. MultiMAP can also be used for batch correction. More detail is available in our [paper](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02565-y). |
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<p align="center"><img src="docs/MultiMAP_schematic.png" width="900"></p> |
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<p align="center"><img src="https://easymed.ai/models/AlyssaS/MultiMAP/git/ci/main/tree/docs/MultiMAP_schematic.png?raw=true" width="900"></p> |
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## Installation |
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## Installation |
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```bash |
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```bash
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pip3 install git+https://github.com/Teichlab/MultiMAP.git |
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pip3 install git+https://github.com/Teichlab/MultiMAP.git
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``` |
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``` |
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## Usage and Documentation |
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## Usage and Documentation |
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MultiMAP offers two functions accepting AnnData objects on input: |
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MultiMAP offers two functions accepting AnnData objects on input:
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- `MultiMAP.Integration()` expects a list of one AnnData per dataset, with the desired dimensionality reduction precomputed and stored in `.obsm`. This allows for refining the initial dimensionality reduction, e.g. if wishing to use `TFIDF_LSI` for ATAC data and PCA for RNA data. |
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- `MultiMAP.Integration()` expects a list of one AnnData per dataset, with the desired dimensionality reduction precomputed and stored in `.obsm`. This allows for refining the initial dimensionality reduction, e.g. if wishing to use `TFIDF_LSI` for ATAC data and PCA for RNA data.
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- `MultiMAP.Batch()` expects a single AnnData object with the dataset information stored in an `.obs` column. This allows for convenient integration with minimal preparation if all datasets can be treated with the same dimensionality reduction. |
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- `MultiMAP.Batch()` expects a single AnnData object with the dataset information stored in an `.obs` column. This allows for convenient integration with minimal preparation if all datasets can be treated with the same dimensionality reduction. |
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There's also an AnnData-independent `MultiMAP.matrix.MultiMAP()` function which operates directly on dimensionality reduction matrices. This requires precomputing all pairwise dimensionality reductions prior to calling MultiMAP. |
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There's also an AnnData-independent `MultiMAP.matrix.MultiMAP()` function which operates directly on dimensionality reduction matrices. This requires precomputing all pairwise dimensionality reductions prior to calling MultiMAP. |
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A tutorial covering both RNA-ATAC integration and RNA-Seq batch correction use can be found [here](https://nbviewer.jupyter.org/github/Teichlab/MultiMAP/blob/master/examples/tutorial.ipynb). |
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A tutorial covering both RNA-ATAC integration and RNA-Seq batch correction use can be found [here](https://nbviewer.jupyter.org/github/Teichlab/MultiMAP/blob/master/examples/tutorial.ipynb). |
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Documentation of the function parameters can be found on [ReadTheDocs](https://multimap.readthedocs.io/en/latest/). |
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Documentation of the function parameters can be found on [ReadTheDocs](https://multimap.readthedocs.io/en/latest/). |
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## Citation |
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## Citation |
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If your work uses MultiMAP, please cite the [paper](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02565-y): |
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If your work uses MultiMAP, please cite the [paper](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02565-y): |
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@article{jain2021multimap, |
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@article{jain2021multimap,
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title={MultiMAP: dimensionality reduction and integration of multimodal data}, |
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title={MultiMAP: dimensionality reduction and integration of multimodal data},
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author={Jain, Mika Sarkin and Polanski, Krzysztof and Conde, Cecilia Dominguez and Chen, Xi and Park, Jongeun and Mamanova, Lira and Knights, Andrew and Botting, Rachel A and Stephenson, Emily and Haniffa, Muzlifah and others}, |
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author={Jain, Mika Sarkin and Polanski, Krzysztof and Conde, Cecilia Dominguez and Chen, Xi and Park, Jongeun and Mamanova, Lira and Knights, Andrew and Botting, Rachel A and Stephenson, Emily and Haniffa, Muzlifah and others},
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journal={Genome biology}, |
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journal={Genome biology},
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volume={22}, |
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volume={22},
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number={1}, |
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number={1},
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pages={1--26}, |
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pages={1--26},
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year={2021}, |
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year={2021},
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publisher={BioMed Central} |
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publisher={BioMed Central}
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} |
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} |
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## Contact |
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## Contact |
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Mika Sarkin Jain - mikasarkinjain@gmail.com \ |
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Mika Sarkin Jain - mikasarkinjain@gmail.com \
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Mirjana Efremova - m.efremova@qmul.ac.uk \ |
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Mirjana Efremova - m.efremova@qmul.ac.uk \
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Sarah Teichmann - st9@sanger.ac.uk |
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Sarah Teichmann - st9@sanger.ac.uk
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Datasets
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