https://github.com/j4c0bs/xfcs
FCS (3.0, 3.1) data and metadata extractor
https://github.com/j4c0bs/xfcs
flow-cytometry flow-cytometry-data
Last synced: about 1 year ago
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FCS (3.0, 3.1) data and metadata extractor
- Host: GitHub
- URL: https://github.com/j4c0bs/xfcs
- Owner: j4c0bs
- License: bsd-2-clause
- Created: 2017-07-23T05:44:45.000Z (almost 9 years ago)
- Default Branch: master
- Last Pushed: 2017-08-08T20:01:50.000Z (almost 9 years ago)
- Last Synced: 2025-03-01T09:48:33.272Z (over 1 year ago)
- Topics: flow-cytometry, flow-cytometry-data
- Language: Python
- Homepage:
- Size: 234 KB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.rst
- License: LICENSE.txt
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README
xfcs
=======
Extract metadata and data from FCS (3.0, 3.1) files.
Data extraction supports file formats:
- Mode: List (L)
- Datatypes: I, F, D
Implemented parameter data set options:
- raw
- channel values
- scale values (log10, gain)
- channel and scale combined into one data set
- fluorescence compensation
- log10 scaled fluorescence compensation
Metadata extraction features:
- support for non-compliant files
- merge or separate csv files
- rolling mean for any keyword with a numeric value
- append new fcs files to previously generated metadata csv file
Interactive dashboard plots using the `xfcsdashboard `_ add-on module.
.. image:: docs/dashboard_preview.png
Installation
------------
Using pip:
::
pip install xfcs
Without pip:
::
python setup.py install
Command Line Usage
------------------
See
`USAGE `_
for expanded details.
To see a list of available commands and arguments, run ''xfcs data --help'' or ''xfcs metadata --help''
::
extract data: xfcs data [options]
extract metadata: xfcs metadata [options]
Requirements
------------
- Python 3.5 or greater
- numpy
- pandas
License
-------
xfcs is released under the BSD 2-clause license. See
`LICENSE `_
for details.