User: kuckunniwid

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kuckunniwid70
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1 month ago
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3 years, 5 months ago
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Posts by kuckunniwid

<prev • 39 results • page 1 of 4 • next >
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Comment: C: Customised piechart for 2 variables
... not answer but a comment: it is called doughnut chart, not a pie chart, and was developed by people who find pie chart not ugly and useless enough. Use stacked barplot or any other type of plot which does not force reader to compare angles or areas. ...
written 5 weeks ago by kuckunniwid70
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Comment: C: Ploidy Correction In NGS cancer data (human)
... They did a great job. I'll try to find the method Zack described in his paper (he cites it as unpublished) about maximum parsimoneous CNA sequence of events reconstruction. Hopefully it will help. ...
written 5 weeks ago by kuckunniwid70
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Comment: C: Ploidy Correction In NGS cancer data (human)
... Thanks! will check sequenza. ...
written 6 weeks ago by kuckunniwid70
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Comment: C: Ploidy Correction In NGS cancer data (human)
... thanks for the answer! do you know any papers from that UCL lab? And I still don't understand what does it mean to adjust for ploidy. Is it "to establish baseline correctly"? ...
written 6 weeks ago by kuckunniwid70
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Comment: C: Ploidy Correction In NGS cancer data (human)
... Yeap, and this is the thing... Samples are rarely clearly integer number ploid, e.g. https://iovs.arvojournals.org/article.aspx?articleid=2518413, fig 2, and like 20 percents of samples are polyploid, so throwing them out would be strange and our collaborators will not understand why we threw away 2 ...
written 6 weeks ago by kuckunniwid70
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Comment: C: Ploidy Correction In NGS cancer data (human)
... Yeah, I am asking about tumors that exhibit such almost whole genome alterations :( I just can not throw them away because they are polyploid and there is no concensus, these samples were obtained with too much efforts from my colleagues. ControlFreec as far as I know does not work with heterogeneou ...
written 6 weeks ago by kuckunniwid70
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Comment: C: Ploidy Correction In NGS cancer data (human)
... I am quite confident in terms of cna calling. What I don't understand is the interpretation. I will try to re formulate my question. When we have tetraploid sample and gene X (and only gene X) has copy number 3 - is it deletion or duplication? How should I transform it to use as input for machine le ...
written 6 weeks ago by kuckunniwid70
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Comment: C: Ploidy Correction In NGS cancer data (human)
... I mean, may be i explained it wrong, but basically my tool identifies diploid parts and perform calling with relation to diploid (just like facets does), so in theory no need for ploidy adjustment, I just thought that such adjustment is performed for better interpretability, not for better calling : ...
written 6 weeks ago by kuckunniwid70
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Comment: C: Ploidy Correction In NGS cancer data (human)
... Thanks for the answer! I use my own tool ClinCNV, it does all these things. I just wander how to interpret the data when I want to put calls in form (sample purity, sample ploidy, gene copy number, ccf of this gene copy number) into machine learning model. Because some ways of adjustment for ploidy ...
written 6 weeks ago by kuckunniwid70
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Ploidy Correction In NGS cancer data (human)
... Hi, I have a callset from cancer NGS data (tumor/normal design, ~100 samples) and I have CNVs called there. Additional complexity is - some samples are close to tri- and tetra-ploid state. I study impact of genomic variants on therapy response. In some papers I've met definition "ploidy corrected ...
ploidy cnv cancer written 6 weeks ago by kuckunniwid70

Latest awards to kuckunniwid

Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: Customised piechart for 2 variables
Scholar 20 months ago, created an answer that has been accepted. For A: Inconsistent Coverage on X chromosome between genders
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Inconsistent Coverage on X chromosome between genders

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