User: Dario Strbenac

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Dario Strbenac1.5k
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Research Associate

Posts by Dario Strbenac

<prev • 222 results • page 1 of 23 • next >
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Answer: A: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
... 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 Strbenac1.5k
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Recommended Read Support Filter for Breakends
... 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 ...
structuralvariantannotation written 11 weeks ago by Dario Strbenac1.5k • updated 7 weeks ago by Daniel Cameron20
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Comment: C: Accounting for Gene Set Overlaps in Goana and Kegga Results
... 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 Strbenac1.5k
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Accounting for Gene Set Overlaps in Goana and Kegga Results
... 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 ...
limma pathway written 3 months ago by Dario Strbenac1.5k • updated 3 months ago by mikhael.manurung200
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Comment: C: Matching TCGA Aliquot ID to UUID or Barcode
... 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 Strbenac1.5k
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Matching TCGA Aliquot ID to UUID or Barcode
... 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? ...
tcgabiolinks tcgautils genomicdatacommons written 5 months ago by Dario Strbenac1.5k • updated 4 months ago by Marcel Ramos ♦♦ 410
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Comment: C: rbind VCF Two Objects Column Names Error
... 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 Strbenac1.5k
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Answer: A: How can I overcome the error of "No residual degrees of freedom in linear model
... 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 Strbenac1.5k
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rbind VCF Two Objects Column Names Error
... 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 ...
variantannotation vcf written 6 months ago by Dario Strbenac1.5k
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Comment: C: Mimic Counting of HTSeq-count Using countOverlaps
... 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 Strbenac1.5k

Latest awards to Dario Strbenac

Voter 4 months ago, voted more than 100 times.
Popular Question 11 months ago, created a question with more than 1,000 views. For TranscriptDb of GENCODE Genes
Scholar 19 months ago, created an answer that has been accepted. For A: Comparison of Column of AnnotatedDataFrame
Popular Question 19 months ago, created a question with more than 1,000 views. For GRanges Constructor With seqlengths
Scholar 2.5 years ago, created an answer that has been accepted. For A: Comparison of Column of AnnotatedDataFrame
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: how to extract read alignments from reads aligning in mulitple locations
Popular Question 2.5 years ago, created a question with more than 1,000 views. For GRanges Constructor With seqlengths
Popular Question 2.5 years ago, created a question with more than 1,000 views. For GRanges Constructor With seqlengths
Popular Question 2.5 years ago, created a question with more than 1,000 views. For GRanges Constructor With seqlengths
Popular Question 2.8 years ago, created a question with more than 1,000 views. For TranscriptDb of GENCODE Genes
Supporter 3.7 years ago, voted at least 25 times.
Scholar 4.1 years ago, created an answer that has been accepted. For A: vcountPattern for Pattern Contained within or Containing Subject
Centurion 6.7 years ago, created 100 posts.

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