fcsparser


Namefcsparser JSON
Version 0.2.8 PyPI version JSON
download
home_pagehttps://www.github.com/eyurtsev/kor
SummaryA python package for reading raw fcs files
upload_time2023-10-17 13:50:21
maintainer
docs_urlNone
authorEugene Yurtsev
requires_python>=3.8.0,<4.0.0
licenseMIT
keywords flow cytometry data analysis cytometry parser data
VCS
bugtrack_url
requirements No requirements were recorded.
Travis-CI No Travis.
coveralls test coverage No coveralls.
            FCSParser
=================


fcsparser is a python package for reading fcs files. 

.. image:: https://github.com/eyurtsev/kor/actions/workflows/test.yml/badge.svg?branch=main&event=push   
   :target: https://github.com/eyurtsev/kor/actions/workflows/test.yml
   :alt: Unit Tests

Install
==================

    $ pip install fcsparser
    
or
    
    $ conda install -c bioconda fcsparser

Using
==================

    >>> import fcsparser
    >>> path = fcsparser.test_sample_path
    >>> meta, data = fcsparser.parse(path, reformat_meta=True)

A more detailed example can be found here: https://github.com/eyurtsev/fcsparser/blob/master/doc/fcsparser_example.ipynb

Features
===================

- **python**: 3.8, 3.9, 3.10, 3.11
- **FCS Formats**: Supports FCS 2.0, 3.0, and 3.1
- **FCS Machines**: BD FACSCalibur, BD LSRFortessa, BD LSR-II, MiltenyiBiotec MACSQuant VYB, Sony SH800

Contributing
=================

Pull requests are greatly appreciated. Missing features include:

1. the ability to apply compensation.
2. a set of transformations (hlog, logicle, etc.) that can be applied.

Also fcs files from more devices and more formats are greatly appreciated, especially if the parser fails for them!

Resources
==================

- **Documentation:** https://github.com/eyurtsev/fcsparser
- **Source Repository:** https://github.com/eyurtsev/fcsparser
- **Comments or questions:** https://github.com/eyurtsev/fcsparser/issues

LICENSE
===================

The MIT License (MIT)

Copyright (c) 2013-2023 Eugene Yurtsev

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.

            

Raw data

            {
    "_id": null,
    "home_page": "https://www.github.com/eyurtsev/kor",
    "name": "fcsparser",
    "maintainer": "",
    "docs_url": null,
    "requires_python": ">=3.8.0,<4.0.0",
    "maintainer_email": "",
    "keywords": "flow cytometry,data analysis,cytometry,parser,data",
    "author": "Eugene Yurtsev",
    "author_email": "eyurtsev@gmail.com",
    "download_url": "https://files.pythonhosted.org/packages/f1/7b/b8decfe3b0e6c2aca4e9069bb80f54960fe6405a6bf63c01a9ca685ba5c6/fcsparser-0.2.8.tar.gz",
    "platform": null,
    "description": "FCSParser\n=================\n\n\nfcsparser is a python package for reading fcs files. \n\n.. image:: https://github.com/eyurtsev/kor/actions/workflows/test.yml/badge.svg?branch=main&event=push   \n   :target: https://github.com/eyurtsev/kor/actions/workflows/test.yml\n   :alt: Unit Tests\n\nInstall\n==================\n\n    $ pip install fcsparser\n    \nor\n    \n    $ conda install -c bioconda fcsparser\n\nUsing\n==================\n\n    >>> import fcsparser\n    >>> path = fcsparser.test_sample_path\n    >>> meta, data = fcsparser.parse(path, reformat_meta=True)\n\nA more detailed example can be found here: https://github.com/eyurtsev/fcsparser/blob/master/doc/fcsparser_example.ipynb\n\nFeatures\n===================\n\n- **python**: 3.8, 3.9, 3.10, 3.11\n- **FCS Formats**: Supports FCS 2.0, 3.0, and 3.1\n- **FCS Machines**: BD FACSCalibur, BD LSRFortessa, BD LSR-II, MiltenyiBiotec MACSQuant VYB, Sony SH800\n\nContributing\n=================\n\nPull requests are greatly appreciated. Missing features include:\n\n1. the ability to apply compensation.\n2. a set of transformations (hlog, logicle, etc.) that can be applied.\n\nAlso fcs files from more devices and more formats are greatly appreciated, especially if the parser fails for them!\n\nResources\n==================\n\n- **Documentation:** https://github.com/eyurtsev/fcsparser\n- **Source Repository:** https://github.com/eyurtsev/fcsparser\n- **Comments or questions:** https://github.com/eyurtsev/fcsparser/issues\n\nLICENSE\n===================\n\nThe MIT License (MIT)\n\nCopyright (c) 2013-2023 Eugene Yurtsev\n\nPermission is hereby granted, free of charge, to any person obtaining a copy\nof this software and associated documentation files (the \"Software\"), to deal\nin the Software without restriction, including without limitation the rights\nto use, copy, modify, merge, publish, distribute, sublicense, and/or sell\ncopies of the Software, and to permit persons to whom the Software is\nfurnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in\nall copies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\nTHE SOFTWARE.\n",
    "bugtrack_url": null,
    "license": "MIT",
    "summary": "A python package for reading raw fcs files",
    "version": "0.2.8",
    "project_urls": {
        "Homepage": "https://www.github.com/eyurtsev/kor",
        "Repository": "https://www.github.com/eyurtsev/kor"
    },
    "split_keywords": [
        "flow cytometry",
        "data analysis",
        "cytometry",
        "parser",
        "data"
    ],
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "blake2b_256": "1e10bfdc8e5b35896d8134a9637ce51c6686f60d8a10fe511de2e07accb8b407",
                "md5": "2d00d118053aac669687790885929031",
                "sha256": "833b02ceff18f34c9304681f5b6675039f5b39a31dfdd9640881f43223bcc2ab"
            },
            "downloads": -1,
            "filename": "fcsparser-0.2.8-py3-none-any.whl",
            "has_sig": false,
            "md5_digest": "2d00d118053aac669687790885929031",
            "packagetype": "bdist_wheel",
            "python_version": "py3",
            "requires_python": ">=3.8.0,<4.0.0",
            "size": 14613064,
            "upload_time": "2023-10-17T13:50:18",
            "upload_time_iso_8601": "2023-10-17T13:50:18.119032Z",
            "url": "https://files.pythonhosted.org/packages/1e/10/bfdc8e5b35896d8134a9637ce51c6686f60d8a10fe511de2e07accb8b407/fcsparser-0.2.8-py3-none-any.whl",
            "yanked": false,
            "yanked_reason": null
        },
        {
            "comment_text": "",
            "digests": {
                "blake2b_256": "f17bb8decfe3b0e6c2aca4e9069bb80f54960fe6405a6bf63c01a9ca685ba5c6",
                "md5": "cbc37bc65ff7385717afabb84ebb15b5",
                "sha256": "df0436bf678df1f4ad3274e55fa06773f884fa45d8329015913a6178d10c73ea"
            },
            "downloads": -1,
            "filename": "fcsparser-0.2.8.tar.gz",
            "has_sig": false,
            "md5_digest": "cbc37bc65ff7385717afabb84ebb15b5",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": ">=3.8.0,<4.0.0",
            "size": 14538608,
            "upload_time": "2023-10-17T13:50:21",
            "upload_time_iso_8601": "2023-10-17T13:50:21.240216Z",
            "url": "https://files.pythonhosted.org/packages/f1/7b/b8decfe3b0e6c2aca4e9069bb80f54960fe6405a6bf63c01a9ca685ba5c6/fcsparser-0.2.8.tar.gz",
            "yanked": false,
            "yanked_reason": null
        }
    ],
    "upload_time": "2023-10-17 13:50:21",
    "github": true,
    "gitlab": false,
    "bitbucket": false,
    "codeberg": false,
    "github_user": "eyurtsev",
    "github_project": "kor",
    "travis_ci": false,
    "coveralls": false,
    "github_actions": true,
    "lcname": "fcsparser"
}
        
Elapsed time: 0.61572s