diffcyt
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lmweber
R package for differential discovery analyses in high-dimensional cytometry data
Hello, Thank you for the package. It is well written. I have a paired-design experiment with different times of visits. I am trying to get DA-GLMM to work on an...
Hi! Thank you for sharing the code. I just have a quick question. I have a list of numbered patients, from ID_001 to ID_120, and two classes. However, these are...
Hi, Thanks for the great package! Does diffcyt allows for settings where estimating associations with a continuous phenotype at the subject level (e.g., BMI of subjects) is of interest, or...
I have a mass cytometry dataset of samples collected from patients with AML (n=30). There is one sample from each patient, and the patients can be divided into two groups...
In my dataset, I have 2 conditions I would like to analyse: - Treatment: Levels A, B and C - Stimulation: Baseline, After Stimulation All of the patients have a...
Hi, I have followed the tutorial and so far all differential expression analyses worked if I did not specify a random variable. This is how the ds_formula2 looks for me....
I was running an analysis based on the CATALYST workflow ran and got an error with `diffcyt()`: ``` Error in SummarizedExperiment(assays = list(counts = n_cells), rowData = row_data, : the...
Hi Lukas, first off, thanks for your work on diffcyt, it's been enormously helpful for my research. I've been mostly using the edgeR option for my differential abundance analysis, but...
Hi @lmweber, Thanks for all your work. I'm currently following the CATALYST workflow and ran into a question when I was trying to get the `createContrast()` for the diffcyt-DA-GLMM to...
