Tutorial:Resources for flow cytometry bioinformatics
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8.8 years ago
Ahill ★ 1.9k

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 Tutorial flow-cytometry • 10k views
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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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Please do not ask questions in old threads. Open a new question, providing code and necessary background information.

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

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3.0 years ago

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