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User: Dario Strbenac
Dario Strbenac • 1.4k
- Reputation:
- 1,420
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- Trusted
- Location:
- Australia
- Last seen:
- 15 hours ago
- Joined:
- 8 years, 10 months ago
- Email:
- d*************@sydney.edu.au
PhD student.
Posts by Dario Strbenac
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1
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101
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... 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 Strbenac • 1.4k
0
votes
0
answers
126
views
0
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... 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 Strbenac • 1.4k
5
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1
answer
141
views
1
answer
... 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 ...
written 5 months ago by
Dario Strbenac • 1.4k
• updated
5 months ago by
Mike Smith • 3.2k
2
votes
1
answer
158
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1
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... 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 Strbenac • 1.4k
1
vote
1
answer
135
views
1
answer
... 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 8 months ago by
Dario Strbenac • 1.4k
• updated
8 months ago by
davide risso • 810
0
votes
0
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124
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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 8 months ago by
Dario Strbenac • 1.4k
0
votes
1
answer
250
views
1
answers
... That's right.
...
written 8 months ago by
Dario Strbenac • 1.4k
0
votes
1
answer
250
views
1
answers
... 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 Strbenac • 1.4k
1
vote
2
answers
206
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 8 months ago by
Dario Strbenac • 1.4k
1
vote
1
answer
250
views
1
answer
... 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 9 months ago by
Dario Strbenac • 1.4k
• updated
8 months ago by
Hervé Pagès ♦♦ 13k
Latest awards to Dario Strbenac
Popular Question
6 months ago,
created a question with more than 1,000 views.
For Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 4 elements
Popular Question
8 months ago,
created a question with more than 1,000 views.
For Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 4 elements
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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