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 intersection or highly-variable 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:
# 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:
pip install PyComplexHeatmap
conda install -c bioconda gprofiler-official
# 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.
Release files for mosaicmpi 2.8.7
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| mosaicmpi-2.8.7.tar.gz | 92.3 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| mosaicmpi-2.8.7-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 188.8 kB
Release files / mosaicmpi-2.8.7.tar.gz
| Download URL | mosaicmpi-2.8.7.tar.gz |
|---|---|
| Size | 92.3 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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No |
| Uploaded via |
twine/6.1.0 CPython/3.12.3
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Release files / mosaicmpi-2.8.7-py3-none-any.whl
| Download URL | mosaicmpi-2.8.7-py3-none-any.whl |
|---|---|
| Size | 96.6 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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No |
| Uploaded via |
twine/6.1.0 CPython/3.12.3
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