flowVS 1.4.2 – Variance Stabilization in Flow Cytometry

flowVS 1.4.2

:: DESCRIPTION

flowVS is a variance-stabilization algorithm that removes the mean-variance correlations from cell populations identified in each fluorescence channel.

::DEVELOPER

Ariful Azad <azadcse at gmail.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R / BioConductor

:: DOWNLOAD

 flowVS

:: MORE INFORMATION

Citation

flowVS: channel-specific variance stabilization in flow cytometry.
Azad A, Rajwa B, Pothen A.
BMC Bioinformatics. 2016 Jul 28;17:291. doi: 10.1186/s12859-016-1083-9.

BayesFlow 0.1 – Latent Modeling of Flow Cytometry Cell Populations

BayesFlow 0.1

:: DESCRIPTION

BayesFlow is a Bayesian hierarchical model, that models the variation across indivuals for clow cytometry data.

::DEVELOPER

Jonas Wallin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Python

:: DOWNLOAD

 BayesFlow

:: MORE INFORMATION

Citation

Erratum to: BayesFlow: latent modeling of flow cytometry cell populations.
Johnsson K, Wallin J, Fontes M.
BMC Bioinformatics. 2016 Mar 31;17(1):149.

flowPeaks 1.12.0 – Fast unsupervised Clustering for Flow Cytometry Data

flowPeaks 1.12.0

:: DESCRIPTION

flowPeaks is a fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means

::DEVELOPER

Yongchao Ge<yongchao.ge at gmail.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • BioConductor/ R

:: DOWNLOAD

 flowPeaks

:: MORE INFORMATION

Citation

flowPeaks: a fast unsupervised clustering for flow cytometry data via K-means and density peak finding.
Ge Y, Sealfon SC.
Bioinformatics. 2012 Aug 1;28(15):2052-8. doi: 10.1093/bioinformatics/bts300

FCS Express 5.01.0060 – Flow Cytometry Tool

FCS Express 5.01.0060

:: DESCRIPTION

FCS Express can rapidly analyze vast amounts of data, with industry leading flow cytometry tools, but we recognize that is only the beginning of the scientific journey. After the basic analysis is complete, you must compile spreadsheets comparing your data to previous experiments, create bar charts and scatter plots to show these differences and create presentations to show your work to others. FCS Express seamlessly takes you from your primary listmode data files to flexible overviews of your entire experiment.

::DEVELOPER

DE NOVO SOFTWARE

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

FCS Express

:: MORE INFORMATION

WEASEL 3.3 – Flow Cytometry Data Analysis

WEASEL 3.3

:: DESCRIPTION

WEASEL is a general purpose flow cytometry data analysis and display program developed at WEHI. As can be seen from the sample screen below, many different display formats are possible as are the extraction of a number of numerical or statistical measures. Multiple flow cytometry standard (FCS) data files can be compared side-by-side on screen and there is facility for fast scanning through collections of data files. Display layouts may be saved as may high quality graphics which may be incorporated into other documents. One of the program’s design parameters was to make operation as simple and intuitive as possible so self instruction should be the best course.

::DEVELOPER

Frank Battye PhD

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX /  Linux
  • Java

:: DOWNLOAD

WEASEL

:: MORE INFORMATION

flowBin 1.6.0 – Combining Multitube Flow Cytometry data by Binning

flowBin 1.6.0

:: DESCRIPTION

flowBin is a parameterisation-free method for combining multitube flow cytometry data into a higher-dimensional form suitable for deep profiling and discovery.

::DEVELOPER

Kieran O’Neill <koneill at bccrc.ca>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux /MacOs
  • R
  • Bioconductor

:: DOWNLOAD

 flowBin

:: MORE INFORMATION

Citation

Deep profiling of multitube flow cytometry data.
O’Neill K, Aghaeepour N, Parker J, Hogge D, Karsan A, Dalal B, Brinkman RR.
Bioinformatics. 2015 Jan 18. pii: btv008.

QUALIFIER 1.15.2 – Qualitiy Control for Gated Flow Cytometry data

QUALIFIER 1.15.2

:: DESCRIPTION

The QUAliFiER package takes advantage of the manual gates to perform an extensive series of statistical quality assessment checks on the gated cell sub-populations while taking into account the structure of the data and the study design to monitor the consistency of population statistics across staining panels, subject, aliquots, channels, or other experimental variables.

::DEVELOPER

Raphael Gottardo’s Research Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX /Windows
  • R package
  • BioConductor

:: DOWNLOAD

 QUALIFIER

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Sep 28;13:252. doi: 10.1186/1471-2105-13-252.
QUAliFiER: an automated pipeline for quality assessment of gated flow cytometry data.
Finak G, Jiang W, Pardo J, Asare A, Gottardo R.

RchyOptimyx 2.10.0 – Optimyzed Cellular Hierarchies for Flow Cytometry

RchyOptimyx 2.10.0

:: DESCRIPTION

RchyOptimyx constructs a hierarchy of cells using flow cytometry for maximization of an external variable (e.g., a clinical outcome or a cytokine response).

::DEVELOPER

Terry Fox Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

  RchyOptimyx

:: MORE INFORMATION

Citation

Cytometry A. 2012 Dec;81(12):1022-30. doi: 10.1002/cyto.a.22209. Epub 2012 Oct 8.
RchyOptimyx: cellular hierarchy optimization for flow cytometry.
Aghaeepour N1, Jalali A, O’Neill K, Chattopadhyay PK, Roederer M, Hoos HH, Brinkman RR.

CYTOWIN 4.31 – Flow Cytometry Analysis Software

CYTOWIN 4.31

:: DESCRIPTION

CYTOWIN is a program designed to analyse flow cytometer data. CYTOWIN can analyse flow cytometer data in one of the following forms : single parameter histograms, two-parameter cytograms and list mode. It can analyze data generated by the following instruments:

  • Coulter:EPICS 5, Profile or Elite ,
  • Becton Dickinson: FACScan, FACSort, FACSAria
  • Cytomation CICERO.

It can also analyse other distributions stored as ASCII files such as Coulter Counter volume distributions. Its main advantages are the speed of processing and the possibility to directly recover statistics in worksheet format.

::DEVELOPER

Daniel Vaulot

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

CYTOWIN

:: MORE INFORMATION

Citation

Vaulot, D. 1989.
CYTOPC: Processing software for flow cytometric data.
Signal and Noise 2:8

flowDensity 1.5.1 – Sequential Flow Cytometry Data Gating

flowDensity 1.5.1

:: DESCRIPTION

flowDensity facilitates reproducible, high-throughput analysis of flow cytometry data by automating a predefined manual gating approach.

::DEVELOPER

M. Jafar Taghiyar, Mehrnoush Malek <mmalekes at bccrc.ca>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 flowDensity

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Oct 16. pii: btu677.
flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification.
Malek M, Taghiyar MJ, Chong L, Finak G, Gottardo R, Brinkman RR.