Tutorial:Resources for flow cytometry bioinformatics

Question

[Ahill]

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

• flowCore http://bioconductor.org/packages/release/bioc/html/flowCore.html
• Pytometry https://pytometry.netlify.app
• CFCS library http://sourceforge.net/projects/flowcyt
• 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 https://support.cytobank.org/hc/en-us/articles/206145157-What-is-Cytobank-
• 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

[shamini.ayyadhury]

Dear Kevin,

I have been trying to use your scDataviz package and I keep running into this error:-

Error in markerExpression(UMAP_tumors, dimColnames = c("UMAP1", "UMAP2"),  : 
  When the input data is a non-SingleCellExperiment object, 'indata' must relate to an expression matrix (cells as columns; genes as rows), while 'layout' must be non-NULL and relate to a 2-dimensional embedding containing columns specified by 'dimColnames'

As I am still new to R, i would be grateful if you can help me out here.

Many thanks.

regards, Shamini A

[ATpoint]

Please do not ask questions in old threads. Open a new question, providing code and necessary background information.

[Kevin Blighe]

Hi Shamini, I had hoped that the error message would be sufficient instruction for you (?)

Answer 1

[Kevin Blighe]

To add to this list, I have been developing some functions for processing CyTOF and flow cytometry data since around 2015. I have built upon / improved them as I became exposed to more of these types of data since then. I have finally produced a 'prototype' R package that will eventually be submitted to Bioconductor:

• scDataviz: single cell dataviz and downstream analyses

These functions also serve scRNA-seq.

Kevin