User: Dario Strbenac
Dario Strbenac • 1.4k
- Reputation:
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- Australia
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- 5 hours ago
- Joined:
- 8 years, 2 months ago
- Email:
- d*************@sydney.edu.au
PhD student.
Posts by Dario Strbenac
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... 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 ...
written 4 weeks ago by
Dario Strbenac • 1.4k
• updated 29 days ago by
davide risso • 740
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... 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 ...
written 4 weeks ago by
Dario Strbenac • 1.4k
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91
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... That's right.
...
written 6 weeks ago by
Dario Strbenac • 1.4k
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91
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... 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 6 weeks ago by
Dario Strbenac • 1.4k
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88
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2
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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 7 weeks ago by
Dario Strbenac • 1.4k
1
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91
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... 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 ...
written 7 weeks ago by
Dario Strbenac • 1.4k
• updated 6 weeks ago by
Hervé Pagès ♦♦ 13k
1
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0
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... 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 ...
written 10 weeks ago by
Dario Strbenac • 1.4k
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1
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181
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... 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 3 months ago by
Dario Strbenac • 1.4k
0
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129
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... 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 4 months ago by
Dario Strbenac • 1.4k
0
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0
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129
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... 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 4 months ago by
Dario Strbenac • 1.4k
Latest awards to Dario Strbenac
Popular Question
10 weeks ago,
created a question with more than 1,000 views.
For GRanges Constructor With seqlengths
Scholar
10 weeks ago,
created an answer that has been accepted.
For A: Comparison of Column of AnnotatedDataFrame
Teacher
12 months ago,
created an answer with at least 3 up-votes.
For A: how to extract read alignments from reads aligning in mulitple locations
Popular Question
12 months ago,
created a question with more than 1,000 views.
For GRanges Constructor With seqlengths
Scholar
12 months ago,
created an answer that has been accepted.
For A: Comparison of Column of AnnotatedDataFrame
Popular Question
12 months ago,
created a question with more than 1,000 views.
For GRanges Constructor With seqlengths
Popular Question
12 months ago,
created a question with more than 1,000 views.
For GRanges Constructor With seqlengths
Popular Question
16 months ago,
created a question with more than 1,000 views.
For TranscriptDb of GENCODE Genes
Supporter
2.3 years ago,
voted at least 25 times.
Scholar
2.7 years ago,
created an answer that has been accepted.
For A: vcountPattern for Pattern Contained within or Containing Subject
Centurion
5.2 years ago,
created 100 posts.
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