User: Dario Strbenac

gravatar for Dario Strbenac
Dario Strbenac1.4k
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Australia
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7 years, 9 months ago
Email:
d*************@sydney.edu.au

PhD student.

Posts by Dario Strbenac

<prev • 190 results • page 2 of 19 • next >
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Vertically Flipped Sashimi Plot
... Is it possible with Gviz to render Sashimi plots for two alignment tracks with one of the plots vertically flipped? This would mean that the zero value was in between the two tracks and the arcs of each track would be pointing out to opposite directions, so the arcs would be joined at the mid-line b ...
gviz sashimi plot written 8 months ago by Dario Strbenac1.4k
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Answer: A: How to get treatment information with TCGAbiolinks?
... This is explained in the software's vignette. It seems that hardly any samples have details recorded about drug treatment, so it doesn't seem possible to incorporate patient treatment into your analysis. Perhaps another relevant dataset might be available from Gene Expression Omnibus and could have ...
written 8 months ago by Dario Strbenac1.4k
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Most Efficient Application of Voom to Regularly Increasing Study
... What is the most efficient usage of voom in a scenario where more batches are arriving at some time in the future? If voom is applied to each batch individually, then, due to filtering of each count matrix on CPM, the resulting normalised value tables of each batch contain a different number of rows ...
limma voom batch effect correction written 10 months ago by Dario Strbenac1.4k • updated 10 months ago by Aaron Lun18k
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Comment: C: plotMDS Input Feature Filtering
... Certainly, I could. I wanted to see if there was an obvious batch effect before I applied batch effect correction, because I like to try and avoid between-sample normalisation if it's there's no clear difference. The first batch has 14 male and 4 female samples, whereas the second has 21 male and 21 ...
written 11 months ago by Dario Strbenac1.4k
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Comment: C: threshold to filter lowly expressed genes
... Indeed, after reading it again, I noticed that I interpreted it incorrectly. ...
written 11 months ago by Dario Strbenac1.4k
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Comment: C: threshold to filter lowly expressed genes
... I think that the current wording is confusing. The explanation states "This ensures that a gene will be retained if it is expressed in both the libraries belonging to any of the six groups.". I read this as the two samples will belong to the same class, whereas the filtering is independent of sample ...
written 11 months ago by Dario Strbenac1.4k
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plotMDS Input Feature Filtering
... When examining the most variable genes for a clinical cancer dataset generated as batches on different days, I notice that the genes are mainly ones located on the X and Y chromosomes such as XIST, UTY, and ZFY. Is it common practice to subset the matrix to remove these before making MDS plots, as t ...
edger exploratory data analysis written 11 months ago by Dario Strbenac1.4k • updated 10 months ago by Gordon Smyth32k
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Comment: C: Importing Gene Symbols with makeTxDbFromGFF
... Another solution is to read the file twice, once with makeTxDbFromGFF and a second time with import.gff3. Then, the matching of IDs is easy and doesn't miss those newly discovered genes which GENCODE has annotated with symbols. ...
written 11 months ago by Dario Strbenac1.4k
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Importing Gene Symbols with makeTxDbFromGFF
... I'd like to import the GENCODE Genes GFF3 file with its gene symbols. By using columns on the TxDb object, it is apparent that only the gene_id field is imported, which has entries such as ENSG00000000003.14.How can I also import the gene_name column, which has values like TSPAN6? ...
genomicfeatures gff3 written 11 months ago by Dario Strbenac1.4k • updated 11 months ago by Valerie Obenchain ♦♦ 6.4k
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Comment: C: TCGAbiolinks query error
... The software currently has some errors. Hopefully, the developers will fix it soon and your problem will be resolved. ...
written 12 months ago by Dario Strbenac1.4k

Latest awards to Dario Strbenac

Popular Question 7 months ago, created a question with more than 1,000 views. For GRanges Constructor With seqlengths
Popular Question 7 months ago, created a question with more than 1,000 views. For GRanges Constructor With seqlengths
Popular Question 11 months ago, created a question with more than 1,000 views. For TranscriptDb of GENCODE Genes
Supporter 22 months ago, voted at least 25 times.
Scholar 2.3 years ago, created an answer that has been accepted. For A: vcountPattern for Pattern Contained within or Containing Subject
Centurion 4.8 years ago, created 100 posts.

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