User: camerond

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camerond0
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Posts by camerond

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How are the MotifbreakR scores calculated, and how do they relate to one another?
... I have been using MotifbreakR to assess out how mutations to transcription factor binding sites disrupt DNA-protein interactions. The analysis went fine but I'm unsure about how the output values relate to one another. Here is the code I used for the analysis which ran fine: MG_results_ADsnp ...
R motifbreakr motifs written 7 months ago by camerond0
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Comment: C: edgeR error when trying to filter peaks with low read counts
... Thanks Aaron. Both for your answers and advice. Your last point is interesting as we are hoping to make comparisons between groups with different library sizes.  I'll have a think about this, and have a better read of your paper in the next few days. ...
written 20 months ago by camerond0
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Comment: C: edgeR error when trying to filter peaks with low read counts
... ... the values are different for the offset in both cases due, no doubt, to the log-library size scaling you mentioned. The part I don't understand fully is your last point: 'adding an appropriate prior count to shrink expression values to a constant value (and thus, the log-fold changes to zero)', ...
written 20 months ago by camerond0
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Comment: C: edgeR error when trying to filter peaks with low read counts
... Hi Aaron, Thanks for the response.  Yes, the lib-size was the issue. Thanks for your help.  I tried updating my version of edgeR (3.18.1) but it doesn't go beyond this version. My R version is not the latest, so I'm sure it's down to that.  Is there any chance you could elaborate a little on you ...
written 20 months ago by camerond0
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Comment: C: edgeR error when trying to filter peaks with low read counts
... ... the values are different for the offset in both cases due, no doubt, to the log-library size scaling you mentioned. The part I don't understand fully is your last point: 'adding an appropriate prior count to shrink expression values to a constant value (and thus, the log-fold changes to zero)', ...
written 20 months ago by camerond0
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edgeR error when trying to filter peaks with low read counts
...   Hello, I have successfully run edgeR on an ATAC-seq dataset to identify differential open chromatin peaks across two cell types. I wanted to normalise for peaks read count, GC content and peak width, so my method was to create a consensus peak set in Diffbind (2 cell types, 3 replicates per cell ...
edger R filtering written 20 months ago by camerond0
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Comment: C: Gvis: Adding colour and transparency to overlaid alignment tracks
... Thanks Robert. That's exactly what I needed.      ...
written 20 months ago by camerond0
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Gvis: Adding colour and transparency to overlaid alignment tracks
... I'm trying to overlay alignment tracks in the Gvis package. I have data for 3 technical replicates from 2 different cell types, so 6 alignment datasets in total.  I have managed to overlay the alignment tracks for the technical replicates in each cell type, so I have 2 composite alignment tracks in ...
gviz alignment tracks written 21 months ago by camerond0 • updated 21 months ago by Robert Ivanek660

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