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mosaicMPI: Mosaic Multi-resolution Program Integration

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mosaicMPI: Mosaic Multi-resolution Program Integration#

version badge PyPI Latest Release Conda Latest Release Documentation status Downloads Stars License DOI:10.1101/2023.08.18.553919

Authors: Ted Verhey, Sorana Morrissy

Contributors: Hyojin Song, Aaron Gillmor, Gurveer Gill, Courtney Hall

mosaicMPI is a Python package for enabling mosaic integration of bulk, single-cell, and spatial expression data through program-level integration. Programs are first discovered using unsupervised deconvolution (consensus non-negative matrix factorization, cNMF) across multiple ranks separately for each dataset. A flexible network-based approach groups similar programs together across resolutions and datasets. Program communities are then interpreted using sample/cell metadata and gene set analyses. Integrative program communities enable metadata transfer across datasets.

⚡Main Features#

Here are just a few of the things that mosaicMPI does well:

  • Identifies interpretable, non-negative programs at multiple resolutions

  • Mosaic integration does not require subsetting features/genes to a shared or overdispersed subset

  • Multi-omics integration without shared sample IDs

  • Incremental integration (adding datasets one at a time) since deconvolution is performed independently on each dataset

  • High performance integration of of datasets with mismatched features (eg. Microarray, RNA-Seq, Proteomics) or sparsity (eg. single-cell vs. bulk)

  • Metadata transfer across datasets

mosaicMPI is usable via:

  • command-line interface for rapid data exploration and integration

  • python interface for extensibility and flexibility

🔧 Install#

🧰 System Requirements#

  • Compatible with OS X, Windows and Linux systems

  • Memory usage depends on size and number of datasets

✨ Latest Release#

Install the package with conda:

# create an environment called mosaic and install
conda create -n mosaic -c conda-forge mosaicmpi
conda activate mosaic

For ssGSEA analysis, you will also need to install GSEApy into the same environment.

# if you have conda (MacOS_x86-64 and Linux only)
conda install -c bioconda gseapy
# Windows and MacOS_ARM64 (M1/2-Chip)
pip install gseapy

📖 Documentation#

Read the documentation.

💭 Getting Help#

For questions arising during use of mosaicMPI, create and browse issues in the GitHub “issues” tab.

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