User: Dario Strbenac
Dario Strbenac • 1.4k
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- Australia
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- 5 days, 11 hours ago
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- 9 years, 1 month ago
- Email:
- d*************@sydney.edu.au
Research Associate
Posts by Dario Strbenac
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... I have output from variant caller Strelka2, which puts SNVs and indels into separate files. I am not able to combine them using `rbind`
```
> class(snv)
[1] "CollapsedVCF"
attr(,"package")
[1] "VariantAnnotation"
> class(ind)
[1] "CollapsedVCF"
attr(,"package")
[1] "VariantAnnotation"
> co ...
written 14 days ago by
Dario Strbenac • 1.4k
0
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1
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61
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1
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... The code example should use `NH` but you have written `NM`. Is there a coercion function that can convert `scaBam`'s list-of-lists data structure into a `GAlignments` or `GAlignmentsPairs` object quickly and concisely? ...
written 19 days ago by
Dario Strbenac • 1.4k
4
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1
answer
61
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1
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... If alignment is done allowing a read to map to multiple locations, is there an easy way to count only the uniquely mapped reads? HTSeq-count "... does not count reads that map to multiple genes.". However, for GAlignments, "... multi-reads (i.e. reads with multiple hits in the reference) won't recei ...
written 20 days ago by
Dario Strbenac • 1.4k
• updated
20 days ago by
Martin Morgan ♦♦ 23k
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2
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107
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... 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 12 weeks ago by
Dario Strbenac • 1.4k
3
votes
2
answers
107
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2
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... 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). ...
written 12 weeks ago by
Dario Strbenac • 1.4k
• updated
12 weeks ago by
Aaron Lun • 24k
0
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1
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141
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... 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 3 months ago by
Dario Strbenac • 1.4k
0
votes
1
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119
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1
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... 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 3 months ago by
Dario Strbenac • 1.4k
1
vote
1
answer
119
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1
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... 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 ...
written 3 months ago by
Dario Strbenac • 1.4k
• updated
3 months ago by
Hotz, Hans-Rudolf • 400
1
vote
1
answer
208
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1
answers
... 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 7 months ago by
Dario Strbenac • 1.4k
0
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0
answers
176
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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 7 months ago by
Dario Strbenac • 1.4k
Latest awards to Dario Strbenac
Popular Question
10 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
12 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
13 months ago,
created an answer that has been accepted.
For A: Comparison of Column of AnnotatedDataFrame
Popular Question
13 months ago,
created a question with more than 1,000 views.
For GRanges Constructor With seqlengths
Teacher
24 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
24 months ago,
created an answer that has been accepted.
For A: Comparison of Column of AnnotatedDataFrame
Popular Question
24 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 GRanges Constructor With seqlengths
Popular Question
24 months ago,
created a question with more than 1,000 views.
For GRanges Constructor With seqlengths
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2.3 years ago,
created a question with more than 1,000 views.
For TranscriptDb of GENCODE Genes
Supporter
3.2 years ago,
voted at least 25 times.
Scholar
3.6 years ago,
created an answer that has been accepted.
For A: vcountPattern for Pattern Contained within or Containing Subject
Centurion
6.2 years ago,
created 100 posts.
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