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Hi,
I am trying to apply a pseudotime analysis to flow cytometry data. These data a processed through a pipeline similar to the CytofWorkflow (Nowicka et al., 2017) and we generate sce objects tha…
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We need to determine an appropriate way to preprocess the data, since protein abundance is not a linear function of the raw measured intensity. In the original Bendall et al. paper (http://www.science…
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Hi,
I'm interested in using SPADE for non-cytometry data and have followed the recommendations in the [FAQ](https://github.com/nolanlab/spade/wiki/FAQ). I have a few questions about the process:
1. I…
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Hi,
I'd like to use pyVIA with flow cytometry data, could you add a tutorial for this kind of data?
Do you have some suggestion about parameters to set?
Thanks you in advance.
Simone
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Hi!
First off, thank you for creating such a great tool!
I'm working with a dataset that includes over 200 markers, and we’re looking to identify the top 5 or 10 markers that define each cluster…
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I have a potentially dumb question. So, as I understand it, we need to discretize the data to work with this package on continuous biological data, such as gene expression or cytometry data. The inbui…
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Hi,
I was wondering if you have anymore insights/guidance on the data transformation.
I have a spectral flow cytometry data set, that a collaborator acquired. I've tried the general 150 co-facto…
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Can one use the warpSet or gaussNorm function of flowStats to normalize high-dimensional CyTOF data? I have such data with a 36-marker panel for 70 samples and I want to reduce batch effects among the…
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Errors remaining:
error - a_study_protein-protein interaction detection_protein microarray.txt
Invalid ISA-TAB: unexpected field Derived Data File found in section transcriptomics_pipeline
warning -…
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For example, one can imagine using Python to carry out some transformations on flow cytometry data, but then use other flow cytometry tools to visualize and further process the data. Since all these …