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 https://isac-net.org
FlowCAP http://flowcap.flowsite.org
Data standards
ISAC standards page https://isac-net.org/page/Data-Standards
FCS 3.1 https://onlinelibrary.wiley.com/doi/10.1002/cyto.a.20825
Gating-ML https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4874733
MIFlowCyt https://isac-net.org/page/MIFlowCyt
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 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4076922
FLOCK http://sourceforge.net/projects/immportflock
SPADE https://github.com/nolanlab/spade
Wanderlust https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4045247/
ACCENSE http://www.cellaccense.com
Phenograph https://github.com/jacoblevine/PhenoGraph
Semi/supervised analysis/visualization
FLAME https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2682540
x-Cyt http://www.broadinstitute.org/mpg/xcyt
Citrus https://github.com/nolanlab/citrus
Other R packages
Bioconductor Flow Cytometry view: http://master.bioconductor.org/packages/release/BiocViews.html#___FlowCytometry
Illustrative highthroughputassays package: http://bioconductor.org/help/workflows/highthroughputassays
Cytofkit https://www.bioconductor.org/packages/3.6/bioc/html/cytofkit.html (status in Bioconductor is now 'deprecated')
OpenCyto https://github.com/RGLab/openCyto
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 (registration required) https://cloud.genepattern.org Browse Modules > Flow Cytometry
Mailing Lists
Purdue cytometry discussion list http://cyto.purdue.edu/hmarchiv
Data repositories
https://flowrepository.org
Dear Kevin,
I have been trying to use your scDataviz package and I keep running into this error:-
As I am still new to R, i would be grateful if you can help me out here.
Many thanks.
regards, Shamini A
Please do not ask questions in old threads. Open a new question, providing code and necessary background information.
Hi Shamini, I had hoped that the error message would be sufficient instruction for you (?)