STAMPede - STAMP data Exploration and Differential Expression

Process & analyse STAMP data with ease! STAMPede is built to handle huge datasets with shallow depth, using syntax familiar to scanpy users.

Table of Contents

1. Installation
2. Usage
3. Citation

Installation

Using conda

conda install -c conda-forge -c bioconda stampede

Using pip

Notes:

• the Pypi package name is stampede-sc. After installation, the package is imported as stampede.
• the Pypi installation requires HDF5.

pip install stampede-sc

Developer installation

Clone the repo

git clone https://github.com/mhlangalab/stampede.git

Change directory into the repo

cd stampede

Create a conda environment

conda env create -n stampede -f requirements.yaml

Activate the conda environment

conda activate stampede

Install the package

pip install -e .

Documentation

Check out our GitHub pages!

Usage

Follow along with the tutorial.ipynb!

Citation

If you used STAMPede in your work, please cite it.