TranSpa

This tool implements Translation-based imputation methods (TransImp) and translation based cell type deconvolution (TransDeconv). Experiments reported in the manuscript are displayed in jupyter notebooks under repo TranSpaAnalysis. Report for TransImp can be accessed from biorxiv with the latest title

Reliable imputation of spatial transcriptome with uncertainty estimation and spatial regularization

Three demo notebooks are also available under the demo folder.

• Different configurations of TransImp applied to SeqFISH dataset dataset
• Exploration for unprobed genes with SeqFISH ST dataset Cell type deconvolution with TransDeconv
• Cell type deconvolution and ST Velocity estimation

Installation

TransImp is available through PyPI. To install, type the following command line and add -U for updates:

pip install -U transpa

Or, download the project and under project root tranSpa/

pip install .

Data

Data used for running the demo notebooks can be downloaed from Zenodo

• seqfish.ipynb and seqfish_unprobed_genes.ipynb requires input data in seqfish.tar.gz
• transDeconv.ipynb requires input data in Mouse_brain.tar.gz

Documentation

Please visit TransImp website for more details.