Tag: Flow Cytometry

flowLearn – Machine-learning algorithm for Gating Flow Cytometry data

flowLearn

:: DESCRIPTION

flowLearn is a semi-supervised approach for the quality-checked identification of cell populations.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

flowLearn

:: MORE INFORMATION

Citation

Lux M, Brinkman RR, Chauve C, Laing A, Lorenc A, Abeler-Dörner L, Hammer B.
flowLearn: fast and precise identification and quality checking of cell populations in flow cytometry.
Bioinformatics. 2018 Jul 1;34(13):2245-2253. doi: 10.1093/bioinformatics/bty082. PMID: 29462241; PMCID: PMC6022609.

SPICE 6.1001 – Data Mining & Visualization Software for Multicolor Flow Cytometry

SPICE 6.1001

:: DESCRIPTION

SPICE is a data mining software application that analyzes large FLOWJO data sets from polychromatic flow cytometry and organizes the normalized data graphically. SPICE enables users to discover potential correlations in their experimental data within complex data sets.

::DEVELOPER

Bioinformatics and Computational Biosciences Branch (BCBB),National Institute of Allergy and Infectious Diseases (NIAID)

:: SCREENSHOTS

SPICE

:: REQUIREMENTS

  • Mac OsX

:: DOWNLOAD

 SPICE

:: MORE INFORMATION

Citation

Cytometry A. 2011 Feb;79(2):167-74. doi: 10.1002/cyto.a.21015. Epub 2011 Jan 7.
SPICE: exploration and analysis of post-cytometric complex multivariate datasets.
Roederer M, Nozzi JL, Nason MC.

FIND 0.31 – Flow Investigation using N-Dimensions

FIND 0.31

:: DESCRIPTION

FIND is a software package designed to facilitate the visualization and analysis of Flow Cytometry data for the scientific target audience, as well as providing a target platform for developers to implement their FC-specific algorithms.

::DEVELOPER

Battelle Center for Mathematical Medicine

:: SCREENSHOTS

find

:: REQUIREMENTS

  • Windows / MacOsX

:: DOWNLOAD

 FIND

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 May 10;12:145. doi: 10.1186/1471-2105-12-145.
FIND: a new software tool and development platform for enhanced multicolor flow analysis.
Dabdoub SM1, Ray WC, Justice SS.

flowDensity 1.27.0 – Sequential Flow Cytometry Data Gating

flowDensity 1.27.0

:: 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.

QUALIFIER 1.26.1 – Qualitiy Control for Gated Flow Cytometry data

QUALIFIER 1.26.1

:: 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 2.32.0 – Optimyzed Cellular Hierarchies for Flow Cytometry

RchyOptimyx 2.32.0

:: 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.

FCS Express 7.06.0015 – Flow Cytometry Tool

FCS Express 7.06.0015

:: 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 3.7.1 – Flow Cytometry Data Analysis

WEASEL 3.7.1

:: 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

flowPeaks 1.38.0 – Fast unsupervised Clustering for Flow Cytometry Data

flowPeaks 1.38.0

:: 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