{"id":28231,"library":"spotiphy","title":"Spotiphy","description":"Integrated pipeline for spatial transcriptomics deconvolution and decomposition to generate pseudo single-cell resolution images. Current version 0.3.1, active development on GitHub.","status":"active","version":"0.3.1","language":"python","source_language":"en","source_url":"https://github.com/jyyulab/Spotiphy","tags":["spatial transcriptomics","deconvolution","single-cell","bioinformatics"],"install":[{"cmd":"pip install spotiphy","lang":"bash","label":"PyPI install"},{"cmd":"pip install git+https://github.com/jyyulab/Spotiphy.git","lang":"bash","label":"Install from GitHub"}],"dependencies":[],"imports":[{"note":"Direct import of module does not give easy access to the main class.","wrong":"import spotiphy","symbol":"Spotiphy","correct":"from spotiphy import Spotiphy"}],"quickstart":{"code":"from spotiphy import Spotiphy\n\n# Initialize with default parameters\nsp = Spotiphy()\n\n# Set required files (paths must exist)\nsp.set_dataset('spatial_folder', 'counts.h5ad')\n\n# Run pipeline\nsp.run()","lang":"python","description":"Basic usage: load Spotiphy class, set dataset, and run."},"warnings":[{"fix":"Ensure the spatial folder contains the required spatial metadata (e.g., tissue_positions_list.csv, scalefactors_json.json).","message":"The set_dataset method expects a folder path and an h5ad file; incorrect paths or missing files cause obscure errors.","severity":"gotcha","affected_versions":"all"},{"fix":"Use `from spotiphy import Spotiphy` instead of old imports.","message":"Older versions (0.1.x) had different API (e.g., `spotiphy.SpotiFlow`). Import path changed in 0.2.0.","severity":"deprecated","affected_versions":"<0.2.0"}],"env_vars":null,"last_verified":"2026-05-09T00:00:00.000Z","next_check":"2026-08-07T00:00:00.000Z","problems":[{"fix":"Run `pip install spotiphy` in the correct Python environment (Python >=3.9).","cause":"Library not installed or installed in wrong environment.","error":"ModuleNotFoundError: No module named 'spotiphy'"},{"fix":"Use `from spotiphy import Spotiphy`.","cause":"Incorrect import; using `import spotiphy` instead of `from spotiphy import Spotiphy`.","error":"AttributeError: module 'spotiphy' has no attribute 'Spotiphy'"}],"ecosystem":"pypi","meta_description":null,"install_score":null,"install_tag":null,"quickstart_score":null,"quickstart_tag":null}