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flowTrans specifications

Information


Unique identifier OMICS_05612
Name flowTrans
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.32.0
Stability Stable
Requirements
methods, stats, R(>=2.11.0), flowCore, flowViz, flowClust
Maintained Yes

Versioning


No version available

Documentation


Publication for flowTrans

flowTrans citations

 (4)
library_books

Immunophenotype Discovery, Hierarchical Organization, and Template Based Classification of Flow Cytometry Samples

2016
PMCID: 5005935
PMID: 27630823
DOI: 10.3389/fonc.2016.00188

[…] orithms have also been discussed in the FC literature (, , ). FLAME () pools cluster centers (mean or medoid) from all samples of a class and clusters these centers to construct global meta-clusters. flowTrans () starts with seed meta-clusters and assigns each cluster to its nearest meta-cluster. Our algorithm is significantly different from both FLAME and flowTrans in several ways. First, FLAME a […]

library_books

Mapping cell populations in flow cytometry data for cross‐sample comparison using the Friedman–Rafsky test statistic as a distance measure

2015
Cytometry
PMCID: 5014134
PMID: 26274018
DOI: 10.1002/cyto.a.22735

[…] d across samples on a per‐channel basis before cell population mapping to further improve the results. Many software and computer programs are available for this data transformation purpose, such as flowTrans , FCSTrans (the method used in this article ), FCS2CSV , and so on, before mapping cell populations in FlowMap‐FR.However, in some experimental scenarios, marker expression shifts reflect im […]

library_books

Flow Cytometry Bioinformatics

2013
PLoS Comput Biol
PMCID: 3867282
PMID: 24363631
DOI: 10.1371/journal.pcbi.1003365

[…] biexponential and Box-Cox transformations, when optimally parameterized, provided the clearest visualization and least variance of cell populations across samples . However, a later comparison of the flowTrans package used in that comparison indicated that it did not parameterize the Logicle transformation in a manner consistent with other implementations, potentially calling those results into qu […]

library_books

A Computational Framework to Emulate the Human Perspective in Flow Cytometric Data Analysis

2012
PLoS One
PMCID: 3341382
PMID: 22563466
DOI: 10.1371/journal.pone.0035693

[…] applied the default logicle transformation to Treg data, for each of the markers Foxp3, CD25 and HLADR, we observed a significant “negative cluster” (). Then we tried to optimize the display with the flowTrans package, but the problem persisted (). To address the problem, we sought an optimal transformation that would remove the negative cluster while making the populations more normally distribut […]


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flowTrans institution(s)
Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA

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