User: tkapell

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tkapell0
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Location:
University of Bonn, Germany
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1 week, 2 days ago
Joined:
11 months, 1 week ago
Email:
t*******@uni-bonn.de

I am a wet lab Immunologist making a career change into the field of Bioinformatics and, in particular, bulk and single-cell transcriptomics. I am interested in the transcriptomic changes observed in human immune cells in health and disease and the molecular networks that are responsible for those.

Posts by tkapell

<prev • 18 results • page 1 of 2 • next >
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Comment: C: GSEA using TFs as the gene set
... Thank you lhuang7. May I ask what is the difference between the two? ...
written 11 days ago by tkapell0
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GSEA using TFs as the gene set
... Hi all,     I have a DE gene dataset and I would like to know which TFs have binding sites at the promoters of these genes. I found a list of 615 human TFs on the GSEA website with the genes they bind to, but my DE gene list is too large to manually test. I then thought to create custom GO terms us ...
gsea transcription factor binding site enrichment analysis written 12 days ago by tkapell0 • updated 11 days ago by lhuang720
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Comment: C: How are the shrunk result data used in DESeq2?
... Thanks for the reply. I now understand why I should use lfcShrink, but wonder whether one can pass all the results arguments in this function as well, e.g. cooksCutoff, independentFiltering, altHypothesis, filterFun. Does lfcShrink run results internally or should I have to run results first and the ...
written 7 months ago by tkapell0
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How are the shrunk result data used in DESeq2?
... I am a bit confused with the "lfcshrink" function in DESeq2. I would assume that one would want to use the shrunk result table in subsequent DE gene analysis, but the DESeq2 manual suggests that lfc shrinkage is only used for data visualisation. Could someone clarify how "results" and "lfcshrink" ar ...
deseq2 lfcshrink written 7 months ago by tkapell0 • updated 7 months ago by Michael Love20k
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Comment: C: How to get DE relative to a fold-change threshold in single factor experiments
... Ok all clear then. Thanks ...
written 8 months ago by tkapell0
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Comment: C: How to get DE relative to a fold-change threshold in single factor experiments
... Yes, that was from the link you posted above. You said that glmQLFit approximations fail with small counts and large dispersions. Can you then elaborate when you would switch to glmFit based on this? ...
written 8 months ago by tkapell0
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Comment: C: How to get DE relative to a fold-change threshold in single factor experiments
... "In summary, while both of the methods will work for your data set, the QL F-test is probably the better choice. There are some situations where the QL F-test doesn't work well - for example, if you don't have replicates, you'd have to supply a fixed dispersion, which defeats the whole point of mode ...
written 8 months ago by tkapell0
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Comment: C: How to get DE relative to a fold-change threshold in single factor experiments
... Thank you, that was really helpful! Would you then recommend a cutoff/threshold for dispersion or counts when you would use glmFit instead of glmQLFit for your DE analysis? ...
written 8 months ago by tkapell0
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Comment: C: How to get DE relative to a fold-change threshold in single factor experiments
... Thank you for the material. I have read the edgeR user's guide and (forgive me if I got it wrong) I understood that: for single factor designs, the exactTest should be used while for multiple factor designs glmFit/glmLRT and more precisely glmQLFit/glmQLFtest should be preferred. For the multiple f ...
written 8 months ago by tkapell0
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How to get DE relative to a fold-change threshold in single factor experiments
... I have a 4 level single factor dataset to analyse with edgeR. I used: tmm<-calcNormFactors(data.dge) y<-estimateDisp(tmm) et<-exactTest(y,pair()) to extract DE genes in the desired comparisons. However, is there an equivalent to glmTreat() in multiple factor experiments to use to get D ...
edger test fisher exact deanalysis written 8 months ago by tkapell0 • updated 8 months ago by Aaron Lun21k

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