User: Dario Strbenac

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

PhD student.

Posts by Dario Strbenac

<prev • 187 results • page 2 of 19 • next >
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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 8 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 8 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 8 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 8 months ago by Dario Strbenac1.4k • updated 8 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 8 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 8 months ago by Dario Strbenac1.4k • updated 8 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 9 months ago by Dario Strbenac1.4k
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Comment: C: Match Pattern Vector to Subject Vector
... Thanks for the suggestion. However,  AhoCorasickSearch  currently doesn't support mismatches nor indels. I doubt that it would be useful for many genomics applications. I notice that my question is basically the same as another recent question. It might be a common use case worth an optimised soluti ...
written 11 months ago by Dario Strbenac1.4k
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Match Pattern Vector to Subject Vector
... Given that vmatchPattern doesn't work with a vector as the pattern and vmatchPDict isn't implemented, are there alternatives in R that don't involve using short read mapping algorithms and building indexes? ...
biostrings biostings written 11 months ago by Dario Strbenac1.4k • updated 11 months ago by Martin Morgan ♦♦ 20k
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Comment: C: findSpliceOverlaps Buffer Error
... I'm glad to know of this limitation with overlapping paired end reads. Indeed, the sample preparation by the core facility was not as good as hoped for. ...
written 11 months ago by Dario Strbenac1.4k

Latest awards to Dario Strbenac

Popular Question 5 months ago, created a question with more than 1,000 views. For GRanges Constructor With seqlengths
Popular Question 5 months ago, created a question with more than 1,000 views. For GRanges Constructor With seqlengths
Popular Question 8 months ago, created a question with more than 1,000 views. For TranscriptDb of GENCODE Genes
Supporter 19 months ago, voted at least 25 times.
Scholar 2.1 years ago, created an answer that has been accepted. For A: vcountPattern for Pattern Contained within or Containing Subject
Centurion 4.6 years ago, created 100 posts.

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