Resources for flow cytometry bioinformatics analysis

28 February 1929

Resources for flow cytometry bioinformatics analysis

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

  • scDataviz: single cell dataviz and downstream analyses: https://github.com/kevinblighe/scDataviz

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