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Tutorial: Resources for flow cytometry bioinformatics

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

Data standards

Parsers, core data access

Unsupervised clustering/visualization

Semi/supervised analysis/visualization

Other R packages

Integrated applications

Utilities

Mailing Lists

Data repositories

single-cell flow-cytometry
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updated by Ram Ram • written by Ahill Ahill

Hi, I am working on Immunophenotyping using flow cytometry. This article is interesting but i have some qurey, can you plz explain me how to bioinformatics useful in Immunophenotyping field.

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written by singh.bioinfo • singh.bioinfo

Hi sakshisingh.bioinfo,

It would be more appropriate to open a separate thread for this question. In addition, your question needs more information to get an accurate answer from the community.

Cheers, Wouter

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written by WouterDeCoster WouterDeCoster

Hi WouterDeCoster,

Thanks for your reply, it is very important to have knowledge that how the approach would be suitable for the research purpose. Specially when it combination of wet lab and dry lab. Already flow cytometry is advanced research tool and how the different approach like an in-silico would be worthy for it.

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written by singh.bioinfo • singh.bioinfo

Hi sakshisingh.bioinfo,

It would be more appropriate to open a separate thread for this question.

Cheers, Wouter

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written by WouterDeCoster WouterDeCoster

Fine WouterDeCoster ! I will put this question publicly as per your suggestion. Thanks and apologies for disturbance.

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written by singh.bioinfo • singh.bioinfo

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

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updated by Kevin Blighe Kevin Blighe • written by shamini.ayyadhury • shamini.ayyadhury

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

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written by ATpoint ATpoint

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

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written by Kevin Blighe Kevin Blighe

1 answer

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:

These functions also serve scRNA-seq.

Kevin

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written by Kevin Blighe Kevin Blighe

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