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unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2026-01-16T20:28:04.816Z","updated_at":"2026-01-16T20:28:05.437Z","avatar_url":"https://github.com/fabilab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![PyPI version](https://badge.fury.io/py/scquill.svg)](https://badge.fury.io/py/scquill)\n\n\u003cimg src=\"https://raw.githubusercontent.com/fabilab/scquill/main/logo.png\" width=\"150\" height=\"150\"\u003e\n\n# scquill\nApproximate any single cell data set, saving \u003e99% of memory and runtime.\n\nIt's pronounced /ˈskwɪɹl̩//, like the [animal](https://en.wiktionary.org/wiki/squirrel).\n\n\n## Approximating a single cell data set\n```python\nimport scquill\n\nq = scquill.Compressor(\n    filename='myscdata.h5ad',\n    output_filename='myapprox.h5',\n    celltype_column=\"cell_annotation\",\n)\n\nq()\n```\n\n## Exploring an approximation\nTo load an approximation:\n```\nimport scquill\n\napp = scquill.Approximation(\n    filename='myapprox.h5',\n)\n```\n\nTo show a dot plot:\n```\nscquill.pl.dotplot(app, ['gene1', 'gene2', 'gene3'])\n```\n\u003cimg src=\"https://raw.githubusercontent.com/fabilab/scquill/main/dotplot.png\" width=\"200\"\u003e\n\n\nTo show a neighborhood plot:\n```\nscquill.pl.neighborhoodplot(app, ['gene1', 'gene2', 'gene3'])\n```\n\u003cimg src=\"https://raw.githubusercontent.com/fabilab/scquill/main/neighborhoodplot.png\" width=\"350\"\u003e\n\nTo show embeddings of cell neighborhoods, similar to single-cell UMAPs:\n\n```\nscquill.pl.embedding(app, ['gene1', 'gene2', 'gene3'])\n```\n\u003cimg src=\"https://raw.githubusercontent.com/fabilab/scquill/main/embeddings.png\" width=\"750\"\u003e\n\n**MORE TO COME**\n\n## Authors\nFabio Zanini @[fabilab](https://fabilab.org)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffabilab%2Fscquill","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffabilab%2Fscquill","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffabilab%2Fscquill/lists"}