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