User: dodausp

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dodausp120
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Denmark/Copenhagen/BRIC
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Posts by dodausp

<prev • 45 results • page 1 of 5 • next >
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Comment: C: How to skip vep-annotating step for vcf2maf
... Hi @Laven9, Did you manage to solve it? ...
written 4 days ago by dodausp120
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Comment: C: Infer somatic mutations without normal control
... Thank you, @CY It does make a lot of sense. ...
written 4 days ago by dodausp120
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Comment: C: Infer somatic mutations without normal control
... Thank you, @CY. And as @Kevin Blighe pointed out above, do you think that by eliminating the common variants found in my samples (cancer only), this could be used as a step to filter out potential germline variants? Would it improve the performance if used jointly with the VEP analysis, or most of i ...
written 4 days ago by dodausp120
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Comment: C: Infer somatic mutations without normal control
... Sorry about this late reply. Somehow some replies were not showing on my feed. Yes, I had read the explanation for that before, but I wasn't still very sure whether by using this would be enough to estimate the somatic variants. And after running VEP, I saw that actually a lot of variants were filte ...
written 4 days ago by dodausp120
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Comment: C: Infer somatic mutations without normal control
... Also, I considered using [Mutect2][1] in the *tumor-only mode*, but it seems that there is still the need to build a PoN. And from what I understood there, a way to call the somatic variants in tumor only samples would be to first create a PoN from all the tumors, identifying the overlapping varian ...
written 10 days ago by dodausp120
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Comment: C: Infer somatic mutations without normal control
... Thanks, @Kevin Blighe! Always very helpful. Yes, I meant "variant". Sorry about that. I corrected it now. (: And yes, I totally agree that this should be only a rough estimation. In the case you're describing here, would enabling the option "Exclude common variants" on the VEP tool achieve that? ...
written 10 days ago by dodausp120
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Comment: C: Infer somatic mutations without normal control
... By using VEP to perform that analysis, what would be the flag that would point to a potential germline variant? Thanks! ...
written 14 days ago by dodausp120
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Comment: C: Complex heatmaps: how not to cluster the slices?
... Have you tried running it with the [default settings][1]? There shouldn't be any splitting there. Heatmap(z_heat) [1]: https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html ...
written 16 days ago by dodausp120
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Answer: A: Complex heatmaps: how not to cluster the slices?
... With that info you provided, first thing I would try was to turn `row_split` argument off. It is likely that the splitting is happening because your `split = dsplit$pathway`. And if you look at the `Heatmap()` function [documentation][1], `row_split=split`. That would be my first guess. Something ...
written 17 days ago by dodausp120
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Answer: A: How to convert maf file format to oncoPrint matrix (ComplexHeatmap package)?
... Have you tried using [maftools][1]? It is a very handy package if you are working with MAF files. It summarizes, analyzes, annotates and visualizes MAF files in a quite nice way. Among many functions, you can [plot your oncoprint][2] there as well. I hope it helps. Good luck! [1]: https://bioc ...
written 17 days ago by dodausp120

Latest awards to dodausp

Supporter 5 months ago, voted at least 25 times.
Popular Question 9 months ago, created a question with more than 1,000 views. For How to set the control group in microarray analysis from illumina data?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Drug interaction not running in MAFtools
Scholar 10 months ago, created an answer that has been accepted. For A: Retrieving miRNA data from Firehose by using RTCGAToolbox
Scholar 10 months ago, created an answer that has been accepted. For A: Retrieving miRNA data from Firehose by using RTCGAToolbox
Popular Question 12 months ago, created a question with more than 1,000 views. For Biobase not running in R 3.5.0

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