New version - 2.1! With the publication of our new manuscript, CODAL in Nature Communications, we have released an updated version of MIRA with reworked and improved topic modeling capacities! If you have used version 1., please take a look at the docs for minor API changes.

    conda install -c bioconda mira-multiome

Multimodal models for Integrated Regulatory Analysis, or MIRA, is a python package for analyzing the dynamic processes of gene regulation using single-cell RNA-seq, ATAC-seq, or multiomics datasets.

MIRA works on top of Scanpy and Anndata to provide a rich, comprehensive framework integrating accessibility and expression data for more insights into your data. MIRA includes methods for:

... And more! Check out the MIRA paper published in Nature Methods. Also, see Getting Started for installation and data preparation instructions.

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Getting Started