{"id":13592159,"url":"https://github.com/gao-lab/Cell_BLAST","last_synced_at":"2025-04-08T23:31:20.990Z","repository":{"id":45836152,"uuid":"177307804","full_name":"gao-lab/Cell_BLAST","owner":"gao-lab","description":"A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.","archived":false,"fork":false,"pushed_at":"2024-07-23T06:57:29.000Z","size":34053,"stargazers_count":82,"open_issues_count":6,"forks_count":13,"subscribers_count":7,"default_branch":"master","last_synced_at":"2024-08-23T05:58:24.194Z","etag":null,"topics":["bioinformatics","deep-learning","single-cell","single-cell-rna-seq"],"latest_commit_sha":null,"homepage":"http://cblast.gao-lab.org","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/gao-lab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2019-03-23T15:44:45.000Z","updated_at":"2024-07-23T06:55:10.000Z","dependencies_parsed_at":"2022-07-19T14:38:47.659Z","dependency_job_id":"27b79d96-f06f-4cc7-9467-d7f070942a15","html_url":"https://github.com/gao-lab/Cell_BLAST","commit_stats":null,"previous_names":[],"tags_count":8,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gao-lab%2FCell_BLAST","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gao-lab%2FCell_BLAST/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gao-lab%2FCell_BLAST/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gao-lab%2FCell_BLAST/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/gao-lab","download_url":"https://codeload.github.com/gao-lab/Cell_BLAST/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":223346553,"owners_count":17130461,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","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":["bioinformatics","deep-learning","single-cell","single-cell-rna-seq"],"created_at":"2024-08-01T16:01:06.387Z","updated_at":"2024-11-06T13:30:28.702Z","avatar_url":"https://github.com/gao-lab.png","language":"Python","funding_links":[],"categories":["Software packages"],"sub_categories":["RNA-seq"],"readme":"# Cell BLAST\n\n[![license-badge](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n[![pypi-badge](https://img.shields.io/pypi/v/Cell-BLAST)](https://pypi.org/project/Cell-BLAST)\n[![docs-badge](https://readthedocs.org/projects/cblast/badge/?version=latest)](https://cblast.readthedocs.io/en/latest/?badge=latest)\n[![build-badge](https://github.com/gao-lab/Cell_BLAST/actions/workflows/build.yml/badge.svg)](https://github.com/gao-lab/Cell_BLAST/actions/workflows/build.yml)\n\nCell BLAST is a cell querying tool for single-cell transcriptomics data.\n\nFor each query cell, it searches for most similar cells in the reference database.\nAnnotations in reference cells, e.g. cell type, can then be transfered to query\ncells based on cell-to-cell similarities. See our\n[publication](https://www.nature.com/articles/s41467-020-17281-7) for details.\n\n## Installing the Python package\n\nWe only support installation via pip right now.\n\nInstallation within virtual environments are recommended, see\n[virtualenv](https://virtualenv.pypa.io/en/latest/) or\n[conda](https://conda.io/docs/user-guide/tasks/manage-environments.html).\n\nFor conda, here's a one-liner to set up an empty environment\nfor installing Cell BLAST:\n\n`conda create -n cb python=3.9 \u0026\u0026 conda activate cb`\n\nThen follow the instructions below to install Cell BLAST:\n\n1. Install Cell BLAST from PyPI by running:\n\n   `pip install Cell-BLAST`\n\n   Or, install an editable dev version by running the following command\n   under the root directory of this repo:\n\n   `flit install -s`\n\n2. Check if the package can be imported in the Python interpreter:\n\n   ```python\n   import Cell_BLAST as cb\n   print(cb.__version__)\n   ```\n\n## Documentation\n\nOnline documentation can be found [here](https://cblast.readthedocs.org/).\n\n## Web-based interface\n\nWe also provide a [Web-based service](http://cblast.gao-lab.org/) for\noff-the-shelf querying of our ACA reference panels.\n\n## Reproduce results in the paper\n\nTo reproduce results, please check out the `rep` branch.\n\n## Contact\n\nFeel free to submit an issue or contact us at\n[cblast@mail.cbi.pku.edu.cn](mailto:cblast@mail.cbi.pku.edu.cn)\nfor problems about the Python package, website or database.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgao-lab%2FCell_BLAST","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgao-lab%2FCell_BLAST","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgao-lab%2FCell_BLAST/lists"}