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User: Dario Strbenac

gravatar for Dario Strbenac
Dario Strbenac1.4k
Reputation:
1,420
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Location:
Australia
Last seen:
15 hours ago
Joined:
8 years, 10 months ago
Email:
d*************@sydney.edu.au

PhD student.

Posts by Dario Strbenac

<prev • 206 results • page 1 of 21 • next >
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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 3 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 3 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 5 months ago by Dario Strbenac1.4k • updated 5 months ago by Mike Smith3.2k
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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 6 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 8 months ago by Dario Strbenac1.4k • updated 8 months ago by davide risso810
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meanVarPlot Ignores Sample Total Count Differences
... I think the example data set below should produce a variance of 0 across the range of means but it doesn't because the library sizes aren't adjusted to be comparable between samples. An adjustment also doesn't happen for the yeast data set on page 8 of the vignette. counts <- matrix(c(seq(100, 1 ...
edaseq meanvarplot written 8 months ago by Dario Strbenac1.4k
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Comment: C: Non-Redundant Edges in Connected Components
... That's right. ...
written 8 months ago by Dario Strbenac1.4k
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Comment: C: Non-Redundant Edges in Connected Components
... A simpler solution is to use the igraph package and use the induced_subgraph function with a vector of vertices belonging to a connected component to create a graph of the connected component. Then, the as_edgelist function converts the graph into a 2-column matrix of edges defining the connected co ...
written 8 months ago by Dario Strbenac1.4k
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Answer: A: Cannot install AUCell 1.2.2
... You need to wait for an update to AUCell to become available. It would have been better if the dependency update to Scenic was made after AUCell was updated. ...
written 8 months ago by Dario Strbenac1.4k
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Non-Redundant Edges in Connected Components
... The connectedComp function determines a list of vertices that belong to a connected component. Is there a quick way to determine the non-redundant edges (i.e. not both A ⇔ B and B ⇔ A but one of these) in each connected component so that correlations (e.g. between pairs of protein measurements) may ...
rbgl written 9 months ago by Dario Strbenac1.4k • updated 8 months ago by Hervé Pagès ♦♦ 13k

Latest awards to Dario Strbenac

Scholar 9 months ago, created an answer that has been accepted. For A: Comparison of Column of AnnotatedDataFrame
Popular Question 9 months ago, created a question with more than 1,000 views. For GRanges Constructor With seqlengths
Teacher 20 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 20 months ago, created an answer that has been accepted. For A: Comparison of Column of AnnotatedDataFrame
Popular Question 20 months ago, created a question with more than 1,000 views. For GRanges Constructor With seqlengths
Popular Question 20 months ago, created a question with more than 1,000 views. For GRanges Constructor With seqlengths
Popular Question 20 months ago, created a question with more than 1,000 views. For GRanges Constructor With seqlengths
Popular Question 24 months ago, created a question with more than 1,000 views. For TranscriptDb of GENCODE Genes
Supporter 2.9 years ago, voted at least 25 times.
Scholar 3.3 years ago, created an answer that has been accepted. For A: vcountPattern for Pattern Contained within or Containing Subject
Centurion 5.8 years ago, created 100 posts.

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