User: Dario Strbenac
Dario Strbenac • 1.5k
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- 9 years, 4 months ago
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- d*************@sydney.edu.au
Research Associate
Posts by Dario Strbenac
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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 2 days ago by
Dario Strbenac • 1.5k
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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 days ago by
Dario Strbenac • 1.5k
• updated
3 days ago by
mikhael.manurung • 160
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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 weeks ago by
Dario Strbenac • 1.5k
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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 weeks ago by
Dario Strbenac • 1.5k
• updated
5 weeks ago by
Marcel Ramos ♦♦ 410
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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 7 weeks ago by
Dario Strbenac • 1.5k
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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 7 weeks ago by
Dario Strbenac • 1.5k
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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 11 weeks ago by
Dario Strbenac • 1.5k
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... 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 12 weeks ago by
Dario Strbenac • 1.5k
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... If alignment is done allowing a read to map to multiple locations, is there an easy way to count only the uniquely mapped reads? HTSeq-count "... does not count reads that map to multiple genes.". However, for GAlignments, "... multi-reads (i.e. reads with multiple hits in the reference) won't recei ...
written 12 weeks ago by
Dario Strbenac • 1.5k
• updated
12 weeks ago by
Martin Morgan ♦♦ 23k
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150
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... With some samples being almost entirely diploid and others being almost entirely tetraploid, Approach 1 wouldn't have many genes to use. It requires a subset of genes that are diploid in all samples. I am doubtful about looping across the samples for Approach 2. Wouldn't that mean using calcNormFact ...
written 5 months ago by
Dario Strbenac • 1.5k
Latest awards to Dario Strbenac
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7 months ago,
created a question with more than 1,000 views.
For TranscriptDb of GENCODE Genes
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12 months ago,
created a question with more than 1,000 views.
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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15 months ago,
created a question with more than 1,000 views.
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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15 months ago,
created an answer that has been accepted.
For A: Comparison of Column of AnnotatedDataFrame
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15 months ago,
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For GRanges Constructor With seqlengths
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2.2 years ago,
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For A: Comparison of Column of AnnotatedDataFrame
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2.2 years ago,
created an answer with at least 3 up-votes.
For A: how to extract read alignments from reads aligning in mulitple locations
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For GRanges Constructor With seqlengths
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For GRanges Constructor With seqlengths
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For GRanges Constructor With seqlengths
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2.5 years ago,
created a question with more than 1,000 views.
For TranscriptDb of GENCODE Genes
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3.4 years ago,
voted at least 25 times.
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3.8 years ago,
created an answer that has been accepted.
For A: vcountPattern for Pattern Contained within or Containing Subject
Centurion
6.3 years ago,
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