mosaicMPI: Mosaic Multi-resolution Program Integration

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 datasets with mismatched features (eg. Microarray, RNA-Seq, Proteomics) or sparsity (eg. single-cell vs. bulk)
• Metadata transfer across datasets

mosaicMPI has two interfaces:

• command-line interface (CLI) with a standardized workflow for rapid data exploration and integration
• python API for greatest flexibility and extensibility

🔧 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:

# if using a fresh conda install
conda init

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

Some analyses require packages from other channels to be installed in the same environment:

• g:Profiler

conda install -c bioconda gprofiler-official

• GSEApy:

# if you have conda (MacOS_x86-64 and Linux only)
conda install -c bioconda gseapy
# Windows and macOS (Apple Silicon)
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.