User: Dario Strbenac

gravatar for Dario Strbenac
Dario Strbenac1.4k
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Australia
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d*************@sydney.edu.au

PhD student.

Posts by Dario Strbenac

<prev • 206 results • page 2 of 21 • next >
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Recommendations for Protein Network Data Structure
... If I would like to represent a protein sub-network, what is the best data structure for it? It has the flat file format:   Hub Interactor ABC XYZ ABC WNT BCL1 RST BCL1 DEF BCL1 ZZY BCL1 CDF I have considere ...
annotationdbi bimap interactome written 7 months ago by Dario Strbenac1.4k
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Comment: C: featureCounts taking 4-10 hours per BAM file?
... The percentage of Successfully aligned fragments is low. It's usually about 80%, not 20%. Quality control of your FASTQ files may reveal some unexpected issues. ...
written 7 months ago by Dario Strbenac1.4k
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Comment: C: How to handle multi-TSS genes in Repitools?
... I wouldn't say that it's the correct approach, but if you are creating a heatmap plot with binPlots, it is best to reduce the number of rows in the heatmap. Having one row for each transcript would make its appearance more complex than necessary. I think including TSS unsupported by reads also could ...
written 8 months ago by Dario Strbenac1.4k
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Comment: C: How to handle multi-TSS genes in Repitools?
... Try processing one sample using RSEM and look at a few genes in IGV to see if the transcript with the majority of assigned reads seems plausible. I'm not convinced of the assertion that there are not enough reads to identify the most highly expressed transcript for each gene. ...
written 8 months ago by Dario Strbenac1.4k
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Answer: A: Splicing analysis with ASpli
... No, you shouldn't concatenate all of the samples belonging to a particular class. You can specify which class each sample belongs to by creating a targets data frame. ASpli also doesn't required paired samples, so there's no reason to force samples from the two classes to be paired somehow. ...
written 9 months ago by Dario Strbenac1.4k
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Comment: C: No BAM option in readAligned from the ShortRead package
... I don't have a recommendation. ...
written 9 months ago by Dario Strbenac1.4k
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Answer: A: No BAM option in readAligned from the ShortRead package
... You should avoid using nucleR for your data analysis. The package depends on RangedData which has been "... has been discouraged in favour of GRanges or GRangesList objects since BioC 2.12, that is, since 2014.". Moreover, RangedData will be deprecated in April and probably removed entirely from IRa ...
written 9 months ago by Dario Strbenac1.4k
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Comment: C: Normalise counts when tumour samples have normal tissue contamination.
... Do you have an estimate of the normal fraction of the tumour samples from a clinician? If the fraction is about the same for all tumour samples, then it's best to do no normalisation. Fold changes would be under-estimated but would be in the correct order. ...
written 9 months ago by Dario Strbenac1.4k
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Answer: A: RUVnormalize- How to output a corrected expression matrix without negative value
... naiveRandRUV ​outputs the dataset with numbers compressed around 0. It's just a characteristic of the method. I like to avoid using RUV unless the PCA or MDS plot indicates that it's necessary. ...
written 11 months ago by Dario Strbenac1.4k
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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 12 months ago by Dario Strbenac1.4k

Latest awards to Dario Strbenac

Scholar 7 months ago, created an answer that has been accepted. For A: Comparison of Column of AnnotatedDataFrame
Popular Question 7 months ago, created a question with more than 1,000 views. For GRanges Constructor With seqlengths
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: how to extract read alignments from reads aligning in mulitple locations
Scholar 17 months ago, created an answer that has been accepted. For A: Comparison of Column of AnnotatedDataFrame
Popular Question 17 months ago, created a question with more than 1,000 views. For GRanges Constructor With seqlengths
Popular Question 17 months ago, created a question with more than 1,000 views. For GRanges Constructor With seqlengths
Popular Question 17 months ago, created a question with more than 1,000 views. For GRanges Constructor With seqlengths
Popular Question 21 months ago, created a question with more than 1,000 views. For TranscriptDb of GENCODE Genes
Supporter 2.7 years ago, voted at least 25 times.
Scholar 3.1 years ago, created an answer that has been accepted. For A: vcountPattern for Pattern Contained within or Containing Subject
Centurion 5.6 years ago, created 100 posts.

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