sodirac 0.1.0

Domain Invariant Representation through Adversarial Calibration (DIRAC), a graph neural network to integrate spatial multi-omic data into a unified domain

DIRAC (Domain Invariant Respresentation through Adversatial Calibration)

Spatially resolved integration of multi-omics with DIRAC highlights cell-specific remodeling

For more details, please check out our publication.

Directory structure

.
├── dirac                  # Main Python package
├── data                    # Data files
├── evaluation              # Method evaluation pipelines
├── experiments             # Experiments and case studies
├── tests                   # Unit tests for the Python package
├── docs                    # Documentation files
├── custom                  # Customized third-party packages
├── packrat                 # Reproducible R environment via packrat
├── env.yaml                # Reproducible Python environment via conda
├── pyproject.toml          # Python package metadata
├── LICENSE
└── README.md

Installation

The spagnns package can be installed via conda using one of the following commands:

conda install -c conda-forge -c bioconda dirac  # CPU only
conda install -c conda-forge -c bioconda dirac pytorch-gpu  # With GPU support

Or, it can also be installed via pip:

pip install spagnns

Installing within a conda environment is recommended.

Usage

Please checkout the documentations and tutorials at dirac.readthedocs.io.