STARMap spatial transcriptome analysis toolkit

The python package of STARMap bioinformatics analysis pipeline.

Installation

# via Pypi (local development)
# cd to the repo folder 
pip install -e .

Usage

# Basic 
from starmap.obj import STARMapDataset, load_data
import starmap.analyze as anz
import starmap.viz as viz

Workflow

cited from Wang(2018), more details @ example

TODO

• Clustering algorithm reproducibility
• Include more example jupyter notebooks
• Conversion support of Scanpy, Seurat
• Batch effect module
• Detailed function documentation

Change Log

• v0.0.1 - Package creation

Reference

1. X Wang*, W E Allen*, M Wright, E Sylwestrak, N Samusik, S Vesuna, K Evans, C Liu, C Ramakrishnan, J Liu, G P Nolan#, F-A Bava#, K Deisseroth#. Three-dimensional intact-tissue-sequencing of single-cell transcriptional states. Science 2018, eaat5691.

*co-first authors; #corresponding authors

License

MIT License