User: Dario Strbenac

gravatar for Dario Strbenac
Dario Strbenac1.4k
Reputation:
1,380
Status:
Trusted
Location:
Australia
Last seen:
5 hours ago
Joined:
8 years, 2 months ago
Email:
d*************@sydney.edu.au

PhD student.

Posts by Dario Strbenac

<prev • 202 results • page 1 of 21 • next >
1
vote
1
answer
34
views
1
answer
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 4 weeks ago by Dario Strbenac1.4k • updated 29 days ago by davide risso740
0
votes
0
answers
32
views
0
answers
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 4 weeks ago by Dario Strbenac1.4k
0
votes
1
answers
91
views
1
answers
Comment: C: Non-Redundant Edges in Connected Components
... That's right. ...
written 6 weeks ago by Dario Strbenac1.4k
0
votes
1
answers
91
views
1
answers
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 6 weeks ago by Dario Strbenac1.4k
0
votes
2
answers
88
views
2
answers
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 Strbenac1.4k
1
vote
1
answer
91
views
1
answer
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 7 weeks ago by Dario Strbenac1.4k • updated 6 weeks ago by Hervé Pagès ♦♦ 13k
1
vote
0
answers
79
views
0
answers
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 10 weeks ago by Dario Strbenac1.4k
0
votes
1
answers
181
views
1
answers
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 3 months ago by Dario Strbenac1.4k
0
votes
0
answers
129
views
0
answers
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 4 months ago by Dario Strbenac1.4k
0
votes
0
answers
129
views
0
answers
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 4 months ago by Dario Strbenac1.4k

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.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 292 users visited in the last hour