xfcs 1.1.6

Extract Flow Cytometry data from FCS files version 3+.

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.

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.