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Tutorial:Resources for flow cytometry bioinformatics
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17 months ago
Ahill ♦ 1.5k
United States

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/Standards.aspx
FCS 3.1 http://isac-net.org/Resources/Standards/FCS3-1.aspx
Gating-ML https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4874733
MIFlowCyt http://isac-net.org/Publications/MIFlowCyt.aspx
Classification Results File Format (CLR) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4874736

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 https://github.com/nolanlab/spade
Wanderlust http://www.c2b2.columbia.edu/danapeerlab/html/wanderlust.html ACCENSE http://www.cellaccense.com
Phenograph https://github.com/jacoblevine/PhenoGraph

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 Astrolabe https://www.astrolabediagnostics.com
FCS Express https://www.denovosoftware.com
Kaluza http://www.beckman.com/coulter-flow-cytometry/software/kaluza-analysis GemStone http://www.vsh.com/products/GemStone/index.asp

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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