Graph-linked unified embedding for unpaired single-cell multi-omics data integration
Project description
GLUE (Graph-Linked Unified Embedding)
Graph-linked unified embedding for single-cell multi-omics data integration
For more details, please check out our publication.
Directory structure
.
├── scglue # 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 scglue
package can be installed either via conda:
conda install -c defaults -c pytorch -c bioconda -c conda-forge -c scglue scglue
Or via pip:
pip install scglue
Installing within a conda environment is recommended.
Usage
Please checkout the documentations and tutorials at scglue.readthedocs.io.
Development
Install scglue in editable form via flit (first install flit via conda or pip if not installed already):
flit install -s
Run unit tests:
pytest --cov="scglue" --cov-report="term-missing" tests [--cpu-only]
Build documentation:
sphinx-build -a -b html docs docs/_build
Reproduce results
-
Checkout the repository to v0.2.0:
git checkout tags/v0.2.0
-
Create a local conda environment using the
env.yaml
file, and then install scglue:conda env create -p conda -f env.yaml && conda activate ./conda flit install -s
-
Set up a project-specific R environment:
packrat::restore() # Packrat should be automatically installed if not available. install.packages("data/download/Saunders-2018/DropSeq.util_2.0.tar.gz", repos = NULL) install.packages("custom/Seurat_4.0.2.tar.gz", lib = "packrat/custom", repos = NULL)
R 4.0.2 was used during the project, but any version above 4.0.0 should be compatible.
-
Follow instructions in
data
to prepare the necessary data. -
Follow instructions in
evaluation
for method evaluation. -
Follow instructions in
experiments
for case studies.
Project details
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