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
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

[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