MultiMAP

MultiMAP is a method for integrating single cell multi-omics. MultiMAP can also be used for batch correction. More detail is available in our preprint.

Installation

We're working on getting the package on pip ASAP. Meanwhile enjoy this placeholder solution!

git clone https://github.com/Teichlab/MultiMAP.git
cd MultiMAP
pip3 install .

Usage and Documentation

MultiMAP offers two functions accepting AnnData objects on input:

• 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.
• 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.

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.

A tutorial covering both RNA-ATAC integration and RNA-Seq batch correction use can be found here.

Documentation of the function parameters can be found on ReadTheDocs.

Citation

If your work uses MultiMAP, please cite the paper:

@article{sarkinjain2021multimap,
  title={MultiMAP: Dimensionality Reduction and Integration of Multimodal Data},
  author={Sarkin Jain, Mika and Dominguez Conde, Cecilia and Polanski, Krzysztof and Chen, Xi and Park, Jongeun and Botting, Rachel 
  and Stephenson, Emily  and Haniffa, Muzlifah and Lamacraft, Austen and Efremova, Mirjana and Teichmann, Sarah},
  doi={https://doi.org/10.1101/2021.02.16.431421},
  journal={BioRxiv},
  year={2021}
}

Contact

Mika Sarkin Jain - mikasarkinjain@gmail.com
Mirjana Efremova - m.efremova@qmul.ac.uk
Sarah Teichmann - st9@sanger.ac.uk