mosaicMPI: Mosaic Multi-resolution Program Integration
Project description
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 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.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for mosaicmpi-2.5.5-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 2413c8cad97128dcf065a2b45ef71a5e4a09c64ec41f77202f5d47410f177a39 |
|
MD5 | cbf437c89606df963fc89f340a00ad13 |
|
BLAKE2b-256 | 7eb6bf4315a2f311108284392e9083b3a3c535e74ee12d77fd0eafd87feb884b |