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.
Here are just a few of the things that mosaicMPI does well:
mosaicMPI is usable via:
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
Read the documentation.
For questions arising during use of mosaicMPI, create and browse issues in the GitHub "issues" tab.