Questions tagged [flow-cytometry]

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FlowSOM multi-step clustering

There are a few different commonly used clustering algorithms within the single-cell space, although Leiden seems to be the top choice these days. FlowSOM is a classic package for analyzing flow ...
burger's user avatar
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Do proper .fcs flow-cytometry files specify the gating hierarchy, so one may calculate cell-counts without specifying it themselves?

Do proper .fcs flow-cytometry files already have the gating hierarchy, so one may calculate cell-counts without extra work? ...
BornPerson's user avatar
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How does one convert "flowJO" flow-cytometry cell-count, etc, bead, etc data into .json or relational-database-management-system compatible files?

How does one convert "flowJO" flow-cytometry cell-count data into ".json" or relational-database-management-system compatible files? The way flow-jo exports is in wide rather than ...
BornPerson's user avatar
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What do "PnBS" and "PnMS" mean in FCS flowCore parameters?

I'm using the flowCore packages to analyze cytometry data, and I am trying to understand all the parameters stored in the FCS file. I've figured out most of the elements, but despite a thorough search ...
RoB's user avatar
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Simultaneously get data from multiple applied gates in flowCore

Using the Bioconductor flowCore package, I'm applying two parallel and non-overlapping gates to a gatingSet directly under "root": ...
gaspanic's user avatar
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What is the correct way of dealing with the analysis of data from flow cytometry?

I would like to detect a change in expression of a molecule present on a cell type by flow cytometry. Assuming I am able to detect, using an antibody, a signal that represents the amount of the ...
gabt's user avatar
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What are negative FSC-A values in flow cytometry data?

I did flow cytometry analysis of E. coli cells 7 hours post inoculation (1% overnight culture in 3ml). I am analysing the FCS3.0 files using the flowCore package in R. I observe that FSC-A has ...
WYSIWYG's user avatar
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Obtain CD (cluster of differentiation) marker expression information

There are 394 CD marker genes. Various resources (BD handbook, Abcam guide) contain information about which cell types express which CD markers. What is the best way to obtain or download this data so ...
Peter's user avatar
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Finding peaks and estimating cell population sizes in multi-dimensional flow cytometry data

Our research institute processes a lot of flow cytometry data, but the produced data is under-utilised due to the effort required to process it. A typical run will produce 5 million events (ideally ...
gringer's user avatar
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