Protocol for atlas-level integration and analysis of single cells

A computational protocol for atlas-level data integration, downstream analysis and linking with phenotypic information from bulk RNA-seq data as performed in Salcher et al. (2022).

Warning: This repository is currently under active development. This means, some parts are still incomplete and there are probably still a lot of mistakes.

Getting started

This repository consists of two parts:

• An online version of the protocol
• A python package (atlas_protocol_scripts) providing utility functions used in the protocol.

For prerequisites and instructions to obtain data and software dependencies for running the tutorial, please see the "before you begin" section in the documentation.

For details on the helper functions, see the API documentation.

Installation

The package with helper functions can be installed from GitHub as follows:

pip install git+https://github.com/icbi-lab/atlas_protocol.git@main

Release notes

See the changelog.

Contact

Please use the issue tracker.

Citation

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