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 1 of 19 • next >
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Comment: C: Changing SVM-Kernal in geNetClassifier function
... No, the packages I mentioned don't output genes selected based on a multi-class criteria. You would need to write the function yourself. Of course, there are many classifiers you can use and different methods will give better classification performance for different datasets.   ...
written 3 days ago by Dario Strbenac1.4k
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Answer: A: Changing SVM-Kernal in geNetClassifier function
... No. It's also bad design that the developers implemented the cost value a constant. The optimal value would differ based on the input dataset. The algorithm basically does feature selection and inputs the chosen genes into to an SVM classifier. You can implement a similar analysis with ClassifyR or ...
written 10 days ago by Dario Strbenac1.4k
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Comment: C: Differential gene expression of longitudinal data
... Is the second visit for every patient qualitatively the same? Why do some patients have three or more visits? ...
written 23 days ago by Dario Strbenac1.4k
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Reproducibility of MultiDataSet Comparison
... In the journal article explaining MultiDataSet, it is claimed that MultiDataSet is better than the competing MultiAssayExperiment because "... MultiAssayExperiment is being developed by a large number of contributors making package improvements (to MultiAssayExperiment) slow and tedious." I wrote to ...
multidataset multiassayexperiment written 11 weeks ago by Dario Strbenac1.4k • updated 10 weeks ago by Levi Waldron380
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Comment: C: Why does total unique map not equal to library size?
... Neither STAR nor HTSeq are Bioconductor software. Biostars is a more relevant forum. ...
written 11 weeks ago by Dario Strbenac1.4k
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Comment: C: how to extract read alignments from reads aligning in mulitple locations
... You imported alignments whereas STAR's summary is in regard to reads. If a read can have more than one alignment, then 9 million reads can result in 20 million alignments because there is a 1:many relationship between them. ...
written 4 months ago by Dario Strbenac1.4k
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Answer: A: how to extract read alignments from reads aligning in mulitple locations
... It's easy. For example, library(GenomicAlignments) ambiguousReads <- readGAlignmentPairs("/users/robert/project/example.bam", param = ScanBamParam(flag = scanBamFlag(isSecondaryAlignment = TRUE))) # Only import multi-mapping reads. library(rtracklayer) genesExonsTranscripts <- import("/user ...
written 4 months ago by Dario Strbenac1.4k
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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 5 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 5 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 7 months ago by Dario Strbenac1.4k • updated 7 months ago by Aaron Lun17k

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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