cnmfsns 1.1.0

cNMF Solution Network Space

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cNMF-SNS: powerful factorization-based multi-omics integration toolkit

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cNMF-SNS (consensus Non-negative Matrix Factorization Solution Network Space) is a Python package enabling integration of bulk, single-cell, and spatial expression data between and within datasets. cNMF provides a robust, unsupervised deconvolution of each dataset into gene expression programs (GEPs). Network-based integration of GEPs enables flexible integration of many datasets across assays (eg. Protein, RNA-Seq) and patient cohorts.

Communities with GEPs from multiple datasets can be annotated with dataset-specific annotations to facilitate interpretation.

:zap: Main Features

Here are just a few of the things that cNMF-SNS does well:

• Integration of expression data does not require subsetting features/genes to a shared subset
• Ideal for incremental integration (adding datasets one at a time) since deconvolution is performed independently on each dataset generating invariant GEPs
• Does not assume the same level of sparsity/depth (single-cell, bulk)
• Identifies interpretable, additive non-negative gene expression programs
• Two interfaces: command-line interface for rapid data exploration and python interface for extensibility and flexibility

:wrench: Install

:lock: Pre-release (Private GitHub Repository)

Before installing cNMF-SNS using pip, it is recommended to first set up a separate conda environment and have conda manage as many dependencies as possible.

conda create --name cnmfsns -c conda-forge python=3.10 anndata pandas numpy scipy matplotlib upsetplot httplib2 tomli tomli-w click pygraphviz python-igraph semantic_version yaml scikit-learn fastcluster scanpy pyyaml gseapy=1.0.3
conda activate cnmfsns

If you use SSH authentication for GitHub, use the following:

pip install git+ssh://[e-mail]/MorrissyLab/cNMF-SNS.git

If you have installed a personal access token from GitHub, you can use:

pip install git+https://<token>@github.com/MorrissyLab/cNMF-SNS.git

:cloud: Public Release

Note: This will work only when cNMF-SNS has been published to PyPI.

pip install cnmfsns

Note: This will work only when cNMF-SNS has been published to conda-forge.

conda install -c conda-forge cnmfsns

:open_book: Documentation

:notebook: Python interface tutorial

To get started, sample proteomics datasets and a Jupyter notebook tutorial is available here.

:computer: Command line interface

See the command line interface documentation.

:thought_balloon: Getting Help

For errors arising during use of cNMF-SNS, create and browse issues in the GitHub "issues" tab.