User: sviatoslav.kendall
sviatoslav.kendall • 470
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Posts by sviatoslav.kendall
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... I'm working with some exome-sequencing data that's been run through a mutation calling pipeline. My goal is determine which samples have deactivating mutations within a subset of genes. Using the [MAF][1] column "Variant_Classification", I've already decided to mutations with values like "stop_gaine ...
written 8 months ago by
sviatoslav.kendall • 470
• updated
8 months ago by
WouterDeCoster ♦ 34k
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... I've got some sequencing data (tumor/normal pairs) that has had mutations called and also been subjected to copy number analysis using [FACETS][1]; these two analyses have been merged such that each mutation has been mapped to a FACETS segment and the associated values.
I want to run an analysis t ...
written 18 months ago by
sviatoslav.kendall • 470
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... I have a list of mutations and want to filter out mutations that are non-diploid or have been amplified or deleted.
The data I'm working with had mutations called using [MuTect][1] and copy-number data produced using [Sequenza][2].
I do not have access to the raw sequencing data so I can't re-ru ...
written 19 months ago by
sviatoslav.kendall • 470
• updated
17 months ago by
Biostar ♦♦ 20
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... I think you should be OK doing that but pay attention to which reference genome you're using. I think the 27K probes might be based on an older build than the 450K. ...
written 20 months ago by
sviatoslav.kendall • 470
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... When I do survival analysis with a continuous variable as the predictor, I use the coxph() function something like this:
coxph_obj = coxph(Surv(my_Data$Survival_Time, my_Data$Survival_Event) ~ my_Data$Continous_Variable)
But here's an older post that you might find helpful: https://www.biostar ...
written 21 months ago by
sviatoslav.kendall • 470
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Comment:
C: Colors in IGV
... The link to IGVs default-color documentation did not work for me but it looks like it was point to [this page][1]
[1]: http://software.broadinstitute.org/software/igv/AlignmentData ...
written 2.0 years ago by
sviatoslav.kendall • 470
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... I'm writing a script that will identify loss of function mutations in a [SNPEFF][1]-annotated MAF file containing point mutations, indels or, in some cases, both.
So far, I've been doing this is by typing up a list of every [Sequence Ontology][2] value that indicates a loss of function:
stop_gaine ...
written 2.2 years ago by
sviatoslav.kendall • 470
• updated
2.1 years ago by
Biostar ♦♦ 20
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... Since you definitely like biology, I suggest you start there by taking bio and bio-relevant classes (chemistry, physics, math, etc). Your declared undergraduate major is far less important to your career than the background knowledge and skills you develop during it - especially for interdisciplinar ...
written 2.2 years ago by
sviatoslav.kendall • 470
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... Yes, a three-level logistic regression on a subset of highly-variable probes seems sensible although I've never done it as formally as all that. My approach has generally been to:
1. Sort loci by decreasing between-samples variance
2. Select the most-variant 5, 10, 25% of loci
3. Plot a heatmap w ...
written 2.3 years ago by
sviatoslav.kendall • 470
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... I would start by restricting my focus to a subset of loci whose beta values show the highest degree of between-samples variance and make some heatmaps with your variables as annotations. Changing up what how many loci you filter out and what sort of clustering method/distance you use will help you s ...
written 2.3 years ago by
sviatoslav.kendall • 470
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