scConnect 1.0.2

scConnect integrate gene expression profiles in scRNA-seq datasets with ligand and receptor interaction information from Guide to pharmacology to construct a graph containing all putative interaction between cell types in the dataset.

scConnect integrate gene expression profiles in scRNA-seq datasets with ligand and receptor interaction information from Guide to pharmacology to construct a graph containing all putative interaction between cell types in the dataset. scConnect integrate well with Scanpy and can be appended to any scanpy analysis pipeline.

Usecases:

• Identify putative cell-cell communication in a tissue

• Infer neuronal networks based on ligand receptor compatability

• Study connectivity changes following treatment

Documentation and tutorial

For a short introduction to how scConnect can be used please check out this tutorial and for information about the API please consult the documentation.

The quickest and easiest way to try out the tutorial is to run through this binder:

Installation

To install the latest stable version install using PYPI

pip install scConnect

This will install all dependencies needed to run the tutorial, and utilize all features of scConnect.

To install the master branch, please clone this repository and install using

cd scConnect/
pip install .

or

pip install git+https://github.com/JonETJakobsson/scConnect

Change log:

1.0.2

• Fixed documentation issues (added .readthedocs.yml)

• removed requirement.txt, build is constructed entirely from setup.py

1.0.1

Bugfixes:

• Fixed a bug in connect.py which cased a crash when connecting ligands and receptors.

1.0.0

Initial release.