diffcyt
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lmweber
R package for differential discovery analyses in high-dimensional cytometry data
Hello I am using diffcyt and CATALYST to analyse flow data. Everything is working very well so far. My dataset is made of samples from individuals who differ by gender...
Hi there I am trying to run a DA analysis (method DA-GLMM). However when I run the analysis I receive the error as seen below. Not too sure whats going...
Hi Lukas I'm running the Cytof Workflow pipeline. I get a very long message (attached below) after running ds_res2
Hi Dr. Weber @lmweber , Is it possible to know the direction of the differential results from diffcyt? I can see which clusters are significant but I don't know the...
Can you please provide a list of the options that the argument markers_to_test can take? I would like to do differential states analysis using the type markers. markers_to_test = id_type_markers...
Hi Dr. Weber, Thanks for the awesome package! My data file is too big to use the built-in plotHeatmap function so I tried the plotDiffHeatMap from the Catalyst package, but...
Hello, I have a feature which contains 8 levels: "aTNF_LPMC" "aINT_LPMC" "aIL_LPMC" "aJAK_LPMC" "5ASA_LPMC" "Steroids_LPMC" "6MP_LPMC" "HC_LPMC". Using contrast
Hello, I have been using CATALYST for my SCE experiment, which are discussed in these issues (please see for experimental details). https://github.com/HelenaLC/CATALYST/issues/119 https://github.com/HelenaLC/CATALYST/issues/121 ## Dimensionality reduction with 4000 cells per...
Hello Lukas, Thank-you for Diffcyt. I had a quick question about setting up contrast matrix for mixed model. I hypothesize that the cell cluster proportions depend on the condition (case-status,...
Hi! I am currently working on analyzing my SCE data, specifically focusing on the CD4+ T cell subpopulations. After clustering, my data shows five distinct subpopulations: CD4+ T naive, CD4+...
