User: Dario Strbenac

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Dario Strbenac1.4k
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Research Associate

Posts by Dario Strbenac

<prev • 214 results • page 1 of 22 • next >
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rbind VCF Two Objects Column Names Error
... 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 ...
variantannotation vcf written 14 days ago by Dario Strbenac1.4k
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Comment: C: Mimic Counting of HTSeq-count Using countOverlaps
... 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 Strbenac1.4k
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Mimic Counting of HTSeq-count Using countOverlaps
... 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 ...
genomicalignments countoverlaps written 20 days ago by Dario Strbenac1.4k • updated 20 days ago by Martin Morgan ♦♦ 23k
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Comment: C: RNA-seq Statstical Models and Transcriptional Amplification
... 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 Strbenac1.4k
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RNA-seq Statstical Models and Transcriptional Amplification
... 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). ...
edger deseq2 transcriptional amplification written 12 weeks ago by Dario Strbenac1.4k • updated 12 weeks ago by Aaron Lun24k
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Comment: C: Paired analysis (tumor vs normal) at three different conditions with EdgeR
... 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 Strbenac1.4k
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Comment: C: qQCReport Missing Plots Described in Documentation
... 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 Strbenac1.4k
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qQCReport Missing Plots Described in Documentation
... 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 ...
quasr written 3 months ago by Dario Strbenac1.4k • updated 3 months ago by Hotz, Hans-Rudolf400
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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 7 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 7 months ago by Dario Strbenac1.4k

Latest awards to Dario Strbenac

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
Popular Question 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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