FlowCytometryTools
-------------------
**Authors**: Jonathan Friedman and `Eugene Yurtsev <http://eyurtsev.mit.edu>`_
.. image:: https://travis-ci.org/eyurtsev/FlowCytometryTools.svg?branch=master
:target: https://travis-ci.org/eyurtsev/FlowCytometryTools
|
FlowCytometryTools is a python package for visualization and analysis of high-throughput flow cytometry data.
* **Intuitive**: provides a simple programmatic interface to work with flow cytometry data
* **Flexible**: can analyze either individual samples or collections of many plates
* **Scalable**: simplifies analysis of high-throughput data using the power of `pandas <http://pandas.pydata.org/>`_
Who is this for?
=====================
FlowCytometryTools is for researchers who want to use the python programming language to analyze flow cytometry data.
The package is specifically tailored for high-throughput analysis. It provides an interface that can directly work with collections of flow cytometry measurements (e.g., 96-well plates).
Basic familiarity with the python programming languages is recommended.
You can find a few example scripts that load and plot flow cytometry data in the `gallery <http://eyurtsev.github.io/FlowCytometryTools/gallery.html>`_ page.
If you like what you see, then proceed to the `installation <http://eyurtsev.github.io/FlowCytometryTools/install.html>`_ page and then
to the `tutorial <http://eyurtsev.github.io/FlowCytometryTools/tutorial.html>`_.
Features
===================
- **Transformations**: hyperlog (hlog), truncated log (tlog), or anything you can dream of ;)
- **Plotting**: 1D, 2D histograms for both single samples and collections (e.g., 96-well plates).
- **Gating**: threshold, interval, quad, polygon gates
- **Subsampling**: easy to subsample to examine only part of a measurement and randomize event order
- **GUI**: simple graphical user interface to draw gates
- **FCS Formats**: Supports FCS 2.0, 3.0, and 3.1
Resources
===================
- **Documentation:** http://eyurtsev.github.io/FlowCytometryTools/
- **Source Repository:** https://github.com/eyurtsev/FlowCytometryTools
- **Comments or questions:** https://github.com/eyurtsev/FlowCytometryTools/issues
Dependencies
===================
For more information about how to obtain these, please see the `installation
<http://eyurtsev.github.io/FlowCytometryTools/install.html>`_ page.
FlowCytometryTools may work with older versions of some of these dependencies, but if
you run into issues, please update the dependencies.
**Required Dependencies**
#. `python <http://www.python.org/getit/>`_ 2.7 (note that python 3.0 or higher are not yet supported!)
#. `decorator <https://pypi.python.org/pypi/decorator>`_
#. `pandas <http://pandas.sourceforge.net/index.html>`__ (Recommended version: 0.12.0 or higher).
#. `matplotlib <http://matplotlib.org/>`__ (Recommended version: 1.13.1 or higher).
#. `scipy <http://www.scipy.org/>`__
**Optional Dependencies**
#. `wx-python <http://wiki.wxpython.org/How%20to%20install%20wxPython>`__ : Used for the FlowCytometryTools GUI.
Alternatives
===================
FlowCytometryTools is not the only open source software for performing data analysis on flow cytometry data.
So if you find that FlowCytometryTools does not suit your needs, take a look at the following software:
* `cytoflow <https://github.com/bpteague/cytoflow>`_: API for python with a GUI
* `fcm <https://pythonhosted.org/fcm/basic.html>`_ : API for python
* `Bioconductor <http://master.bioconductor.org/>`_ : API for the R programming language
* `FlowPy <http://flowpy.wikidot.com/>`_ : GUI
* `cyflogic <http://www.cyflogic.com/>`_ : GUI
* `Flowing Software <http://www.flowingsoftware.com/>`_ : GUI
Changes
=====================
v0.4.5, 2015-10-31
+ Sample fcs files now included with installation
+ Mostly maintenance (tests, configuration files, etc.)
v0.4.4, 2015-09-06
** Repository moved to github **
Enhancements:
+ added an experimental web-based backend for drawing gates. Use FCMeasurement.view_inteactively(backend='webagg').
+ col first enumerator for forming an ordered fcs file collection (Yoav Ram)
Bug fixes:
+ FCPlate.from_dir ID_kwargs match against full path, not just filename (Nick Bolten)
+ fcs parser can read larger fcs files and handles blank headers (Ben Roth)
v0.4.3, 2014-12-05
+ ENHC: Automatically determine bin location when plotting plates.
+ Fix for Accuri V6 FCS (Ben Roth)
+ Fix for xlim/ylim when plotting 2d histograms
v0.4.2, 2014-10-08
+ FCS parser can handle more formats
+ Updated documentation
v0.4.1, 2014-09-13
+ Bug fixes for GUI
+ Now works with matplotlib 1.4.0
+ Added documentation and examples to gallery
v0.4.0, 2014-06-05
+ Updates in documentation
+ Added experimental view() function
+ Renamed old view() function into -> view_interactively()
+ Added queueing to help when dealing with large quantities of data.
+ Histogram plots should work with pandas (0.14.0) & matplotlib (1.3.1).
v0.3.6, 2014-02-11
+ Mostly updates in documentation
v0.3.5, 2014-01-19
+ Boost in speed for transformations on collections of measurements (like 96-well plates).
+ Much of the documentation has been updated and improved.
+ Improved GUI.
v0.3.0, 2013-10-27 Initial Release
LICENSE
===================
The MIT License (MIT)
Copyright (c) 2013-2015 Eugene Yurtsev and Jonathan Friedman
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.
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FlowCytometryTools-0.4.5.tar.gz (60个子文件)
FlowCytometryTools-0.4.5
setup.cfg 159B
README.rst 6KB
FlowCytometryTools.egg-info
dependency_links.txt 1B
PKG-INFO 8KB
SOURCES.txt 3KB
top_level.txt 19B
requires.txt 61B
PKG-INFO 8KB
FlowCytometryTools
IO
__init__.py 0B
fcsreader.py 19KB
tests
test_fcs_reader.py 20KB
__init__.py 0B
data
FlowCytometers
corrupted
corrupted.fcs 10B
HTS_BD_LSR-II
HTS_BD_LSR_II_Mixed_Specimen_001_D6_D06.fcs 644KB
FACSCaliburHTS
Sample_Well_A02.fcs 587KB
Fortessa
FCS_3.0_Fortessa_PBS_Specimen_001_A1_A01.fcs 500KB
MiltenyiBiotec
FCS3.1
EY_2013-07-19_PBS_FCS_3.1_Well_A1.001.fcs 867KB
SG_2014-09-26_Duplicate_Names.fcs 288KB
EY_2013-07-19_PBS_FCS_3.1_Custom_Add_Well_A1.001.fcs 867KB
EY_2013-07-19_PBS_FCS_3.1_Custom_Without_Add_Well_A1.001.fcs 745KB
FCS2.0
EY_2013-07-19_PBS_FCS_2.0_Custom_Without_Add_Well_A1.001.fcs 628KB
FCS3.0
FCS3.0_Custom_Compatible.fcs 627KB
fake_large_fcs
fake_large_fcs.fcs 500KB
Plate03
NoDescription.fcs 627KB
Plate01
RFP_Well_A6.fcs 627KB
YFP_Well_A7.fcs 627KB
CFP_Well_A4.fcs 627KB
RFP_Well_A3.fcs 627KB
RFP_Well_B3.fcs 627KB
CFP_Well_B4.fcs 627KB
YFP_Well_C7.fcs 627KB
Plate02
Mixed_Well_H12.001.fcs 627KB
Mixed_Well_H1.001.fcs 627KB
Mixed_Well_H7.001.fcs 627KB
Mixed_Well_H3.001.fcs 627KB
test_transforms.py 4KB
_version.py 18B
__init__.py 532B
_doc.py 54B
core
common_doc.py 8KB
gates.py 15KB
graph.py 3KB
__init__.py 0B
containers.py 24KB
bases.py 39KB
transforms.py 11KB
GUI
fc_widget.py 31KB
__init__.py 0B
wx_backend
wireframe.py 8KB
__init__.py 0B
gui.py 4KB
webagg_backend
__init__.py 0B
gui.py 9KB
requirements.txt 97B
CHANGES.txt 1KB
README.txt 6KB
LICENSE.txt 1KB
MANIFEST.in 35B
setup.py 3KB
devel_requirements_py27.txt 543B
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