User: David_emir

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David_emir380
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Posts by David_emir

<prev • 182 results • page 1 of 19 • next >
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Comment: C: Quantification of cell cluster in Single cell data
... Thanks a lot for sharing such valuable information. Going forward, is there a way I can use my Seurat Object with CyTOF? ...
written 13 days ago by David_emir380
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Quantification of cell cluster in Single cell data
... 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][1], they have quantified the immune cell dist ...
wilcoxon rna-seq single cell seurat written 13 days ago by David_emir380
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Differentials Expressed Genes from each state in Monocle 2
... Hi there, I know that we can use differentialGeneTest to find genes that are most differentially expressed across the states by using the formula "~State". However, in the resulting data frame, there is no indication of the state number w.r.t. a given gene. Is it possible to get an extra column wi ...
dge monocle2 state single cell written 28 days ago by David_emir380
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CMS subtype identification in Single cell data
... Hi All, Is it possible to identify CMS subtypes for Single-cell data (Seurat object)? I am having ~ 50000 single cells data and using Seurat for the analysis. I am interested in CMS subtyping, is it possible to use CMScaller on single-cell and if yes how can I used Seurat object (counts) as an inpu ...
cmscaller single cell rna-seq written 6 weeks ago by David_emir380 • updated 6 weeks ago by jared.andrews077.6k
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Comment: C: Statistical test on Single-cell clusters(cell types)
... Thanks a lot for your help Kevin, so in. my case the inputs would be no of cells in a particular cell type , say CD4-TREG cell count in Normal would be my a=423 ? ...
written 10 weeks ago by David_emir380
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Comment: C: Statistical test on Single-cell clusters(cell types)
... Hi Kevin, Sorry for that not so clear question. I have 5-cell types identified (the excell snapshot is just for the illustration) - B-cell, Myeloid cell, T-cell, Epithelial, Stromal cell. and [according to this paper][1] they conducted Statistical comparisons of Gini coefficients across compartment ...
written 10 weeks ago by David_emir380
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Statistical test on Single-cell clusters(cell types)
... Hi All, I have identified 5 different cell types from a single cell cluster, we have also identified a number of cells present in each condition(i.e. in Normal and Tumor clusters). I wanted to conduct statistical testing of differences in Gini coefficients between tumour and non-malignant compartme ...
statistical exact permutation test single cell written 10 weeks ago by David_emir380
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Comment: C: Plotting heatmap of Marker genes in each celltypes in Seurat
... Thanks a lot for your kind help, i am trying this code. ...
written 11 weeks ago by David_emir380
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Comment: C: Plotting heatmap of Marker genes in each celltypes in Seurat
... Can you please share any script for this, i am a biologist, my hold on R is very Limited. ...
written 11 weeks ago by David_emir380
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Comment: C: Plotting heatmap of Marker genes in each celltypes in Seurat
... Thanks a lot for such a fast reply, I tried with DoHeatmap, but i couldn't add Tissue/Donor/Sample Info to the Heatmap. I couldn't produce heatmap wth all the cell type markers, my graph will become very cluttery and it's difficult to read. ...
written 11 weeks ago by David_emir380

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