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Flow Cytometry Bioinformatics

Resources for Flow Cytometry Bioinformatics

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

Data standards
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

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
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 http://cytospade.org
Wanderlust http://www.c2b2.columbia.edu/danapeerlab/html/wanderlust.html

Semi/supervised analysis/visualization
FLAME http://www.broadinstitute.org/cancer/software/genepattern/modules/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.
OpenCyto http://opencyto.org

Integrated applications
FlowJo http://www.flowjo.com
CytoBank http://cytobank.org
FCS Express https://www.denovosoftware.com

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