The python package of STARMap bioinformatics analysis pipeline.
# via Pypi (local development)
# cd to the repo folder
pip install -e .# Basic
from starmap.obj import STARMapDataset, load_data
import starmap.analyze as anz
import starmap.viz as viz
- Clustering algorithm reproducibility
- Include more example jupyter notebooks
- Conversion support of Scanpy, Seurat
- Batch effect module
- Detailed function documentation
- v0.0.1 - Package creation
- 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