User: Dario Strbenac

gravatar for Dario Strbenac
Dario Strbenac1.4k
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Australia
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6 days, 16 hours ago
Joined:
8 years, 12 months ago
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d*************@sydney.edu.au

PhD student.

Posts by Dario Strbenac

<prev • 211 results • page 1 of 22 • next >
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Comment: C: RNA-seq Statstical Models and Transcriptional Amplification
... With some samples being almost entirely diploid and others being almost entirely tetraploid, Approach 1 wouldn't have many genes to use. It requires a subset of genes that are diploid in all samples. I am doubtful about looping across the samples for Approach 2. Wouldn't that mean using calcNormFact ...
written 29 days ago by Dario Strbenac1.4k
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RNA-seq Statstical Models and Transcriptional Amplification
... Transcriptional amplification is the phenomenon where the majority of genes in a sample are increased in expression. An overview of it and the statistical implications is found in [Cell][1]. [Recent research][2] found that about 30% of primary cancers have evidence of genome doubling (tetraploidy). ...
edger deseq2 transcriptional amplification written 4 weeks ago by Dario Strbenac1.4k • updated 4 weeks ago by Aaron Lun23k
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Comment: C: Paired analysis (tumor vs normal) at three different conditions with EdgeR
... It might be worth mentioning that the design matrix shown in the question also is correct but it's a bit harder to think about which coefficient to look at for which comparison of interest. ...
written 7 weeks ago by Dario Strbenac1.4k
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Comment: C: qQCReport Missing Plots Described in Documentation
... But the documentation `?qQCReport` provides a list of seven plots which may be generated for any BAM file and an eighth plot which is for BAM files containing paired reads. The test file I used has paired reads samtools view -c -f 1 Rsamtools/extdata/ex1.bam 3307 So, I expect to get **eigh ...
written 7 weeks ago by Dario Strbenac1.4k
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qQCReport Missing Plots Described in Documentation
... According to the documentation, there are eight kinds of plots generated by `qQCReport`. However, I only see four. library(QuasR) testFile <- system.file("extdata", "ex1.bam", package="Rsamtools") qQCReport(testFile, "testQC.pdf") Can the function's result be changed to match the do ...
quasr written 7 weeks ago by Dario Strbenac1.4k • updated 7 weeks ago by Hotz, Hans-Rudolf400
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Answer: A: Difference in TCGA RNAseq expression values between GDC harmonized and legacy da
... Because the reference genome and data processing methods are different. In older TCGA data sets, the reads are mapped to hg19. However, in Genomic Data Commons, the reads are mapped to hg38. Also, RSEM was previously used to estimate the abundances of genes, which includes the estimation of the loca ...
written 5 months ago by Dario Strbenac1.4k
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Comment: C: How to monitor the performance of MS-based omics data?
... There's no package that gives quality control metrics for all of the different varieties of proteomics assays. You could rephrase your question to specify if you are considering DDA, DIA or SRM proteomics. ...
written 5 months ago by Dario Strbenac1.4k
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Converting UniProt Identifier Into Representative Gene Symbol
... In UniProt, an entry such as Q8N4C6 has Gene: NIN but in the Gene Names field Name: NIN Synonyms:KIAA1565 If I select the genes column, I get both names. > select(up, "Q8N4C6", "GENES", "UNIPROTKB") Getting extra data for Q8N4C6 'select()' returned 1:1 mapping between keys and columns UNIPR ...
uniprot.ws written 7 months ago by Dario Strbenac1.4k • updated 7 months ago by Mike Smith3.4k
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Answer: A: Looking for code showing how estimateDispersions works.
... The getMethod function does that for S4 methods. The code of estimateDispersions is displayed in the R console by executing getMethod(estimateDispersions, "DESeqDataSet"). The options you could specify for the second argument of getMethod are listed in the output of showMethods("estimateDispersions" ...
written 8 months ago by Dario Strbenac1.4k
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Mean-Variance Plot for Normalised Counts
... A SeqExpressionSet can store unnormalised counts and normalised counts, but it only seems to be possible to plot the unnormalised counts by meanVarPlot. It would be useful to be able to plot normalised counts to visualise the effect of applying a normalisation method (e.g. DESeq2's varianceStabilizi ...
edaseq meanvarplot written 10 months ago by Dario Strbenac1.4k • updated 10 months ago by davide risso810

Latest awards to Dario Strbenac

Scholar 11 months ago, created an answer that has been accepted. For A: Comparison of Column of AnnotatedDataFrame
Popular Question 11 months ago, created a question with more than 1,000 views. For GRanges Constructor With seqlengths
Teacher 22 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 22 months ago, created an answer that has been accepted. For A: Comparison of Column of AnnotatedDataFrame
Popular Question 22 months ago, created a question with more than 1,000 views. For GRanges Constructor With seqlengths
Popular Question 22 months ago, created a question with more than 1,000 views. For GRanges Constructor With seqlengths
Popular Question 22 months ago, created a question with more than 1,000 views. For GRanges Constructor With seqlengths
Popular Question 2.2 years ago, created a question with more than 1,000 views. For TranscriptDb of GENCODE Genes
Supporter 3.0 years ago, voted at least 25 times.
Scholar 3.5 years ago, created an answer that has been accepted. For A: vcountPattern for Pattern Contained within or Containing Subject
Centurion 6.0 years ago, created 100 posts.

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