Tutorial: Resources for flow cytometry bioinformatics
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gravatar for Ahill
4.0 years ago by
Ahill1.1k
United States
Ahill1.1k wrote:

The need for bioinformatics expertise in flow cytometry is increasing exponentially as the size and complexity of flow datasets grow.  I thought it would be worthwhile to post links to some tools and resources that may be beneficial for bioinformaticians getting starting with flow cytometry.  The list is highly biased and far from complete, so please feel free to add/comment.

Resources for flow cytometry bioinformatics

Community portals
ISAC http://isac-net.org/home.aspx
FlowCAP http://flowcap.flowsite.org

Data standards
ISAC standards page http://isac-net.org/Resources-for-Cytometrists/Data-Standards.aspx
FCS 3.1 http://isac-net.org/images/stories/documents/Standards/fcs3.1_normativespecification_20090813.pdf
Gating-ML http://flowcyt.sourceforge.net/gating
MIFlowCyt http://flowcyt.sourceforge.net/miflowcyt
Classification Results File Format (CLR) http://isac-net.org/PDFS/65/659585c7-9ef4-4152-829c-859aad25aafb.pdf

Parsers, core data access
CFCS library http://sourceforge.net/projects/flowcyt
flowCore  http://bioconductor.org/packages/release/bioc/html/flowCore.html
Python FCM https://pythonhosted.org/fcm/

Unsupervised clustering/visualization
t-SNE https://lvdmaaten.github.io/tsne
VISNE http://www.c2b2.columbia.edu/danapeerlab/html/cyt.html
FLOCK http://sourceforge.net/projects/immportflock
SPADE http://www.bioconductor.org/packages/release/bioc/html/spade.html
CytoSPADE https://github.com/nolanlab/cytospade
Wanderlust http://www.c2b2.columbia.edu/danapeerlab/html/wanderlust.html
ACCENSE http://www.cellaccense.com
Phenograph http://www.c2b2.columbia.edu/danapeerlab/html/phenograph.html

Semi/supervised analysis/visualization
FLAME http://software.broadinstitute.org/cancer/software/genepattern/FLAME
x-Cyt http://www.broadinstitute.org/mpg/xcyt
Citrus https://github.com/nolanlab/citrus

Other R packages
An ever-growing list, to get started go to:
http://bioconductor.org/help/workflows/highthroughputassays and scroll down to the "flow cytometry" section.
Cytofkit https://www.bioconductor.org/packages/release/bioc/html/cytofkit.html
OpenCyto http://opencyto.org

Integrated applications
FlowJo http://www.flowjo.com
CytoBank http://cytobank.org
FCS Express https://www.denovosoftware.com
Kaluza http://www.beckman.com/coulter-flow-cytometry/software/kaluza-analysis

Utilities
BD flow tool index http://www.bdbiosciences.com/research/multicolor/tools/index.jsp
GenePattern Flow Cytometry Suite

Mailing Lists
Purdue cytometry discussion list http://cyto.purdue.edu/hmarchiv

Data repositories
https://flowrepository.org

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