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Possible data:
- [Bystander CD8+ T cells are abundant and phenotypically distinct in human tumour infiltrates](https://www.ncbi.nlm.nih.gov/pubmed/29769722): https://flowrepository.org/id/FR-FCM-ZY…
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Can we use BERMUDA for mass cytometry (CyTOF) data? Unlike scRNA seq. data, CyTOF data may have only 20-40 variables (markers).
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I want to start off by mentioning how much I love scanpy. I recommend this package to everyone I know who is doing single cell sequencing. I love how PAGA and UMAP can be integrated together. PAGA mak…
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Hi, I believe that the function of "cytof_cluster" does not contain Rphenograph_k. When I run in R, I received this error:
> Cluster_PhenoGraph
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Error: Invalid target location for cytof qc report chosen. Please try again.
this is the error in the shiny app
Warning in if (class(cytof_qc_report_dir) != "integer") { :
the condition has lengt…
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Hello,
I had a general question about using MOFA. I recently tried using MOFA to explore some proteomic (359 features) and CyTOF (37 features) in a cohort of 89 patient specimens. The data were nor…
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Hi,
I get an error when I run the following:
BatchAdjust(
basedir="P:/LiU/Postdok/Projekt/GraMS/Resultat/Analysis/CyTOF/3_BatchAdjustedFiles/",
outdir="P:/LiU/Postdok/Projekt/GraMS/Resultat/…
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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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I have manually curated my populations in FlowJo.
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Dear authors,
Thanks for developing such a great package for dealing with the batch effects and multi-panel integration. While studying the vignette, I have difficulties to make my data similar to …