Flow cytometry software - Revision history

Murray: /* Weasel */

2010-04-22T01:20:18Z

Weasel

← Older revision		Revision as of 01:20, 22 April 2010
Line 24:		Line 24:

	This is a basic package that has a variety of plotting tools, but doesn't seem to have nearly as much functionality as FlowJo. The user interface was pretty crude.		This is a basic package that has a variety of plotting tools, but doesn't seem to have nearly as much functionality as FlowJo. The user interface was pretty crude.
			* http://www.wehi.edu.au/faculty/advanced_research_technologies/flow_cytometry/weasel_for_flow_cytometry_data_analysis/

	=== Flow ===		=== Flow ===

Murray: /* Open source/free packages */

2010-04-22T01:19:34Z

Open source/free packages

← Older revision		Revision as of 01:19, 22 April 2010
Line 24:		Line 24:

	This is a basic package that has a variety of plotting tools, but doesn't seem to have nearly as much functionality as FlowJo. The user interface was pretty crude.		This is a basic package that has a variety of plotting tools, but doesn't seem to have nearly as much functionality as FlowJo. The user interface was pretty crude.

			=== Flow ===
			"Flow is an open source software tool for flow cytometry analysis that integrates ontology, statistics and visualization for the classification and comparison of multi-color flow cytometry data sets. Together, these provide powerful new tools for the experimentalist or clinician to analyze flow cytometry data in a different way; one we hope will complement and perhaps one day supersede the traditional strategy of sequential gating."
			* https://galen.dulci.duhs.duke.edu/flow/

	=== BioConductor ===		=== BioConductor ===
Line 31:		Line 35:
	* The plot at the right shows an example of a series of histograms at different timepints. SSC-A is (roughly) the cell volume, FITC-A is the UPR response reporter and mCherry-A is a constitutive fluorescent protein. Produced using the densityplot() function in the flowViz library.		* The plot at the right shows an example of a series of histograms at different timepints. SSC-A is (roughly) the cell volume, FITC-A is the UPR response reporter and mCherry-A is a constitutive fluorescent protein. Produced using the densityplot() function in the flowViz library.
	* The iFlow package is a more visual interface with some basic functions for loading and plotting data (roughly comparable to Weasel).		* The iFlow package is a more visual interface with some basic functions for loading and plotting data (roughly comparable to Weasel).
			* http://bioconductor.org/

	== Toolboxes ==		== Toolboxes ==

Murray: /* Python */

2010-04-22T01:17:46Z

Python

← Older revision		Revision as of 01:17, 22 April 2010
Line 41:		Line 41:

	=== Python ===		=== Python ===
			* Similar to MATLAB, there appear to be a couple of efforts at interacting with raw data:
			** [http://flowpy.wikidot.com/ FlowPy] - read FCS files into python and allow data filtering

	=== R ===		=== R ===
	* See description of BioConductor package above.		* See description of BioConductor package above.

Murray: /* R */

2010-04-22T01:11:01Z

← Older revision		Revision as of 01:11, 22 April 2010
Line 43:		Line 43:

	=== R ===		=== R ===
	See description of BioConductor package above.		* See description of BioConductor package above.

Murray: /* Python */

2010-04-22T01:10:49Z

Python

← Older revision		Revision as of 01:10, 22 April 2010
Line 41:		Line 41:

	=== Python ===		=== Python ===

			=== R ===
			See description of BioConductor package above.

Murray: /* FCS Express */

2010-04-22T01:10:09Z

FCS Express

← Older revision		Revision as of 01:10, 22 April 2010
Line 16:		Line 16:

	Software by De Novo Software, sold through BD Biosciences. Lite version sells for $300, pro version cells for $800 (standalone license). Windows only.		Software by De Novo Software, sold through BD Biosciences. Lite version sells for $300, pro version cells for $800 (standalone license). Windows only.
			* Looks fairly full featured. Similar to FlowJo in look and feel.
			* Couldn't see how to get the type of plot that I am looking for (no obivous time series functionality)

	== Open source/free packages ==		== Open source/free packages ==

Murray: /* FlowJo */

2010-04-22T00:56:42Z

FlowJo

← Older revision		Revision as of 00:56, 22 April 2010
Line 12:		Line 12:

	The software costs about $1500 for a node-locked license or key-based license.		The software costs about $1500 for a node-locked license or key-based license.

			=== FCS Express ===

			Software by De Novo Software, sold through BD Biosciences. Lite version sells for $300, pro version cells for $800 (standalone license). Windows only.

	== Open source/free packages ==		== Open source/free packages ==

Murray at 00:49, 22 April 2010

2010-04-22T00:49:35Z

← Older revision		Revision as of 00:49, 22 April 2010
Line 1:		Line 1:
	This page contains notes on flow cytometry software that I found while trying to analyze some data from UCSF. Mainly for internal usage, but figured I would put it online in case others needed it.		{{righttoc}}This page contains notes on flow cytometry software that I found while trying to analyze some data from UCSF. Mainly for internal usage, but figured I would put it online in case others needed it.

			To try out this software, I have been using a data set collected with Ignacio Zuleta that consisted of a portion of the yeast deletion library with a constitute reporter plus a unfolded protein response (UPR) reporter. The cells were initially sampled and then DTT was added to trigger the unfolded protein response. For additional samples were then taken, at roughly equal intervals of time. We would like to see how the response of the cells varied as a function of time across the different deletion strains.

	== Commercial packages ==		== Commercial packages ==

Murray at 00:46, 22 April 2010

2010-04-22T00:46:30Z

← Older revision		Revision as of 00:46, 22 April 2010
Line 17:		Line 17:
	This is a basic package that has a variety of plotting tools, but doesn't seem to have nearly as much functionality as FlowJo. The user interface was pretty crude.		This is a basic package that has a variety of plotting tools, but doesn't seem to have nearly as much functionality as FlowJo. The user interface was pretty crude.

	=== BioConductor ~~"flow cytometry" workflow~~ ===		=== BioConductor ===

	[[Image:e9-time.png\|right\|300px]]		[[Image:e9-time.png\|right\|300px]]

Murray: /* BioConductor "flow cytometry" workflow */

2010-04-22T00:45:02Z

BioConductor "flow cytometry" workflow

← Older revision		Revision as of 00:45, 22 April 2010
Line 19:		Line 19:
	=== BioConductor "flow cytometry" workflow ===		=== BioConductor "flow cytometry" workflow ===

	[[Image:e9-time.png\|right\|~~100px~~]]		[[Image:e9-time.png\|right\|300px]]
	The BioConductor software suite is a set of R packages that includes a number of tools for reading and manipulating flow cytometry data. The basic libraries handle reading FCS files, maintaining dataframes consisting of collections of FCS data, and a variety of analysis and plotting tools. The iFlow package is a more visual interface with some basic functions for loading and plotting data (roughly comparable to Weasel).		The BioConductor software suite is a set of R packages that includes a number of tools for reading and manipulating flow cytometry data. The basic libraries handle reading FCS files, maintaining dataframes consisting of collections of FCS data, and a variety of analysis and plotting tools.
			* The plot at the right shows an example of a series of histograms at different timepints. SSC-A is (roughly) the cell volume, FITC-A is the UPR response reporter and mCherry-A is a constitutive fluorescent protein. Produced using the densityplot() function in the flowViz library.
			* The iFlow package is a more visual interface with some basic functions for loading and plotting data (roughly comparable to Weasel).

	== Toolboxes ==		== Toolboxes ==