User: Dario Strbenac

gravatar for Dario Strbenac
Dario Strbenac1.3k
Reputation:
1,330
Status:
Trusted
Location:
Australia
Last seen:
13 hours ago
Joined:
7 years, 3 months ago
Email:
d*************@sydney.edu.au

PhD student.

Posts by Dario Strbenac

<prev • 182 results • page 1 of 19 • next >
0
votes
1
answers
87
views
1
answers
Comment: C: how to extract read alignments from reads aligning in mulitple locations
... You imported alignments whereas STAR's summary is in regard to reads. If a read can have more than one alignment, then 9 million reads can result in 20 million alignments because there is a 1:many relationship between them. ...
written 22 days ago by Dario Strbenac1.3k
0
votes
1
answers
87
views
1
answers
Answer: A: how to extract read alignments from reads aligning in mulitple locations
... It's easy. For example, library(GenomicAlignments) ambiguousReads <- readGAlignmentPairs("/users/robert/project/example.bam", param = ScanBamParam(flag = scanBamFlag(isSecondaryAlignment = TRUE))) # Only import multi-mapping reads. library(rtracklayer) genesExonsTranscripts <- import("/user ...
written 23 days ago by Dario Strbenac1.3k
0
votes
0
answers
52
views
0
answers
Vertically Flipped Sashimi Plot
... Is it possible with Gviz to render Sashimi plots for two alignment tracks with one of the plots vertically flipped? This would mean that the zero value was in between the two tracks and the arcs of each track would be pointing out to opposite directions, so the arcs would be joined at the mid-line b ...
gviz sashimi plot written 4 weeks ago by Dario Strbenac1.3k
0
votes
1
answers
78
views
1
answers
Answer: A: How to get treatment information with TCGAbiolinks?
... This is explained in the software's vignette. It seems that hardly any samples have details recorded about drug treatment, so it doesn't seem possible to incorporate patient treatment into your analysis. Perhaps another relevant dataset might be available from Gene Expression Omnibus and could have ...
written 5 weeks ago by Dario Strbenac1.3k
1
vote
1
answer
169
views
1
answer
Most Efficient Application of Voom to Regularly Increasing Study
... What is the most efficient usage of voom in a scenario where more batches are arriving at some time in the future? If voom is applied to each batch individually, then, due to filtering of each count matrix on CPM, the resulting normalised value tables of each batch contain a different number of rows ...
limma voom batch effect correction written 3 months ago by Dario Strbenac1.3k • updated 3 months ago by Aaron Lun15k
0
votes
2
answers
202
views
2
answers
Comment: C: plotMDS Input Feature Filtering
... Certainly, I could. I wanted to see if there was an obvious batch effect before I applied batch effect correction, because I like to try and avoid between-sample normalisation if it's there's no clear difference. The first batch has 14 male and 4 female samples, whereas the second has 21 male and 21 ...
written 4 months ago by Dario Strbenac1.3k
0
votes
1
answers
350
views
1
answers
Comment: C: threshold to filter lowly expressed genes
... Indeed, after reading it again, I noticed that I interpreted it incorrectly. ...
written 4 months ago by Dario Strbenac1.3k
0
votes
1
answers
350
views
1
answers
Comment: C: threshold to filter lowly expressed genes
... I think that the current wording is confusing. The explanation states "This ensures that a gene will be retained if it is expressed in both the libraries belonging to any of the six groups.". I read this as the two samples will belong to the same class, whereas the filtering is independent of sample ...
written 4 months ago by Dario Strbenac1.3k
4
votes
2
answers
202
views
2
answers
plotMDS Input Feature Filtering
... When examining the most variable genes for a clinical cancer dataset generated as batches on different days, I notice that the genes are mainly ones located on the X and Y chromosomes such as XIST, UTY, and ZFY. Is it common practice to subset the matrix to remove these before making MDS plots, as t ...
edger exploratory data analysis written 4 months ago by Dario Strbenac1.3k • updated 4 months ago by Gordon Smyth30k
0
votes
1
answers
161
views
1
answers
Comment: C: Importing Gene Symbols with makeTxDbFromGFF
... Another solution is to read the file twice, once with makeTxDbFromGFF and a second time with import.gff3. Then, the matching of IDs is easy and doesn't miss those newly discovered genes which GENCODE has annotated with symbols. ...
written 4 months ago by Dario Strbenac1.3k

Latest awards to Dario Strbenac

Popular Question 29 days ago, created a question with more than 1,000 views. For GRanges Constructor With seqlengths
Popular Question 4 weeks ago, created a question with more than 1,000 views. For GRanges Constructor With seqlengths
Popular Question 4 months ago, created a question with more than 1,000 views. For TranscriptDb of GENCODE Genes
Supporter 15 months ago, voted at least 25 times.
Scholar 21 months ago, created an answer that has been accepted. For A: vcountPattern for Pattern Contained within or Containing Subject
Centurion 4.3 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: 296 users visited in the last hour