This repository contains jupyter notebooks to reproduce the results and figures from treeArches. treeArches is a framework around two existing methods: scArches and scHPL.
If you want to reproduce the complete results, you will have to install scArches and scHPL. If you just want to reproduce the figures, you can download the latent spaces we created from Zenodo.
treeArches is automatically installed when installing scArches. Check this link for more information about installing scArches.
Documentation and tutorials can be found in the scArches documentation and the scHPL github. The PBMC reproducibility notebook is also a vignette that guides you through the possible functionalities.
For citation and further information please refer to the publication.