singlecell-cookbook 0.3.0

A collection of tools for analyzing single-cell genomics data.

singlecell-cookbook

A collection of tools for analyzing single-cell genomics data.

Installation

You can install the package using pip:

pip install singlecell-cookbook

For development installation:

git clone https://github.com/argearriojas/singlecell-cookbook.git
cd singlecell-cookbook
pip install -e ".[dev]"

R Dependencies

Some features (like pseudobulk analysis) require R and specific R packages. To use these features:

1. Install the required R packages in R:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install(c("edgeR", "MAST"))

2. Install the R dependencies in Python:

pip install "singlecell-cookbook[r]"

Documentation

Documentation is available at Read the Docs.

Development

To set up the development environment:

1. Clone the repository
2. Install development dependencies: pip install -e ".[dev]"
3. Install pre-commit hooks: pre-commit install

License

TBD. We need to assess the license according to the imported packages.

Author

Argenis Arriojas ([e-mail])