mosaicmpi 2.1.4

mosaicMPI: Mosaic Multi-resolution Program Integration

mosaicMPI: mosaic multi-resolution program integration

Authors: Ted Verhey, Heewon Seo, Sorana Morrissy

Contributors: Hyojin Song, Aaron Gillmor, Courtney Hall

mosaicMPI is a Python package enabling mosaic integration of bulk, single-cell, and spatial expression data through program-level integration. Programs are first discovered using consensus non-negative matrix factorization and then integrated using a flexible network-based approach to group similar programs together across resolutions and datasets. Program communities are then interpreted using sample/cell metadata and classical 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
• Ideal for incremental integration (adding datasets one at a time) since deconvolution is performed independently on each dataset
• Integration performs well even when the datasets have mismatched features (eg. Microarray, RNA-Seq, Proteomics) or sparsity (eg single-cell vs bulk RNA-Seq and ATAC-Seq)
• Metadata transfer across datasets
• Command-line interface for rapid data exploration and python interface for extensibility and flexibility

🔧 Install

🧰 System Requirements

• Compatible with and tested on 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 errors arising during use of mosaicMPI, create and browse issues in the GitHub "issues" tab.