Quantification of cell cluster in Single cell data
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6 months ago
David_emir ▴ 390

Hi All,

I have a single cell data from cancer patients and I have analysed the data using Seurat. Now, I wanted to do quantification of cell cluster frequency representation among patient groups. Many papers have used different methods. in this paper, they have quantified the immune cell distribution across clusters and comparison of patient groups. For each cluster, the average fraction of cells from each patient, the paper says and I quote "...The statistical analysis compares control and +CPI colitis patient groups. p < 0.05, *p < 0.01, two-sided Wilcoxon test group is shown, after normalization for total input cell numbers per patient " I did write to the authors for more details and I am still waiting for their reply. Quantification of cells in each cluster

I am looking to do the same analysis for our cancer data, please let me know if there are some codes or packages available which takes the input of surat object and does quantification of cell cluster frequency and generates the plots. Thanks a lot for your kind help,

Stay safe,

Dave.

RNA-Seq single cell seurat Wilcoxon • 258 views
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That is a differential abundance analysis. See e.g. in chapter 14 of https://osca.bioconductor.org/multi-sample-comparisons.html or check the CyTOF package from Bioconductor.

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Thanks a lot for sharing such valuable information. Going forward, is there a way I can use my Seurat Object with CyTOF?

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