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Extract Flow Cytometry data from FCS files version 3+.

Project description

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.
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.

Project details


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Source Distribution

xfcs-1.1.6.tar.gz (142.8 kB view hashes)

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