User: Dario Strbenac
Dario Strbenac • 1.5k
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- Email:
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Research Associate
Posts by Dario Strbenac
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1
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102
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... It seems that the genes which you mention are not being detected as outliers, otherwise they would have p-values of `NA`. You can set the value of `cooksCutoff` to a number smaller than 0.99, which will cause more genes to be eliminated from statistical testing. edgeR has a similar approach which us ...
written 10 weeks ago by
Dario Strbenac • 1.5k
2
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1
answer
98
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1
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... What is the most similar summary to VF for breakpoints that is available for breakends? I want to make a rule that determines whether a breakend is detected or not detected for each sample. I am considering using BANSR + BANRP > 0, but am not confident. Or, is QUAL more suitable? May some common ...
written 11 weeks ago by
Dario Strbenac • 1.5k
• updated
7 weeks ago by
Daniel Cameron • 20
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1
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103
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... Thanks for the suggestion. REVIGO works only for gene ontology, so won't be suited to KEGG pathways. `emapplot` is a good suggestion for visualising the problem but doesn't adjust the statistical modelling to correct for it. ...
written 3 months ago by
Dario Strbenac • 1.5k
2
votes
1
answer
103
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1
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... Is there a technique to resolve the correlation introduced into gene set results from having gene sets which have similar components? For example, if the top results are
## Pathway N Up Down P.Up P.Down
## path:hsa05169 Epstei ...
written 3 months ago by
Dario Strbenac • 1.5k
• updated
3 months ago by
mikhael.manurung • 200
1
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2
answers
310
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... It looks like the function takes a barcode as input and returns the aliquot ID. What about converting an aliquot ID to a barcode? ...
written 5 months ago by
Dario Strbenac • 1.5k
5
votes
2
answers
310
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... Genomic Data Commons hosts [a gene-wise copy number summary][1] for each cancer, which has genes as rows and samples as columns. The column headings are aliquot UUIDs. How may these be matched to other data types, such as a MAF file of SNVs which contains TCGA barcodes as the sample identifier?
...
written 5 months ago by
Dario Strbenac • 1.5k
• updated
4 months ago by
Marcel Ramos ♦♦ 410
0
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0
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161
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... I made a [request for an accessible VCF file created by Strelka2][1] and then got sidetracked.
[1]: https://github.com/Illumina/strelka/issues/131
But, I did notice that some of the INFO and FORMAT fields in the SNV and indel VCF files were different, which is the likely explanation for the erro ...
written 5 months ago by
Dario Strbenac • 1.5k
2
votes
1
answer
197
views
1
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... I suppose that there is a distinct sample ID for each of your 735 samples. You don't want to have `SampleID` as a term in your model formula. You ought to include `Batch`, though. ...
written 5 months ago by
Dario Strbenac • 1.5k
0
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161
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... I have output from variant caller Strelka2, which puts SNVs and indels into separate files. I am not able to combine them using `rbind`
```
> class(snv)
[1] "CollapsedVCF"
attr(,"package")
[1] "VariantAnnotation"
> class(ind)
[1] "CollapsedVCF"
attr(,"package")
[1] "VariantAnnotation"
> co ...
written 6 months ago by
Dario Strbenac • 1.5k
0
votes
1
answer
180
views
1
answers
... The code example should use `NH` but you have written `NM`. Is there a coercion function that can convert `scaBam`'s list-of-lists data structure into a `GAlignments` or `GAlignmentsPairs` object quickly and concisely? ...
written 6 months ago by
Dario Strbenac • 1.5k
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11 months ago,
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For TranscriptDb of GENCODE Genes
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For Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 4 elements
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For Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 4 elements
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For A: Comparison of Column of AnnotatedDataFrame
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For GRanges Constructor With seqlengths
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For A: how to extract read alignments from reads aligning in mulitple locations
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For TranscriptDb of GENCODE Genes
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For A: vcountPattern for Pattern Contained within or Containing Subject
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