User: kristoffer.vittingseerup
- Reputation:
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- European Union
- Last seen:
- 1 year, 1 month ago
- Joined:
- 4 years, 5 months ago
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Posts by kristoffer.vittingseerup
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... There are loads of examples where the switch is between a coding and a non-coding transcript - see fx figure 4 in our article.
Unfortunately apart from the current 3 possibilities: 1) Analysis with CPAT (verifying the coding potential). 2) Looking at structural differences (lengths, number of exons ...
written 14 months ago by
kristoffer.vittingseerup • 20
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... I have (naturally since I'm the authour) used IsoformSwitchAnalyzeR quite a lot. IsoformSwitchAnalyzeR directly supports data from Salmon (use both abundances and counts as described here) and allows a wide range of analysis for Isoform Switches as well as alternative splicing both on individual gen ...
written 14 months ago by
kristoffer.vittingseerup • 20
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... This could very well be the problem - the easiest way to figure this out is by doing a MA plot (x=mean expression over all samples, y= log2FC between condition) - it should be fairly symmetric - else the normalisation did not work.
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written 23 months ago by
kristoffer.vittingseerup • 20
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... How did you quantify the genes (which tool)? And which excat database of gene models did you use for the quantification?
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written 23 months ago by
kristoffer.vittingseerup • 20
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Comment:
C: Updates to BiocStyle formatting
... Awesome job! Are there also updates to "html_vignette" ?
...
written 23 months ago by
kristoffer.vittingseerup • 20
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... The easiest thing is probably to use edgeR. To calculate RPKM you need two things:
1) The count data (which you have)
2) The length of the genes.
You can then construct a DGElist with edgeR as follows:
myDGEList <- DGEList( counts= expressionMatrix , genes= geneDataFrame )
where th ...
written 23 months ago by
kristoffer.vittingseerup • 20
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... I very much agree but I do however think there are two other uses for (ERCC-) spikeins:
1) (Extreme) Cases where there are large changes in the RNA composition (such as knock down/out of decay factors etc)
2) For selecting expression cutoffs - since we know the exact concentration of the spikeins it ...
written 23 months ago by
kristoffer.vittingseerup • 20
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... That sounds extremely usefull - both the feature level test but also the complex designs! Looking forward to try it!
...
written 2.3 years ago by
kristoffer.vittingseerup • 20
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... I have just read the DRIMSeq article ( https://f1000research.com/articles/5-1356/v2 ) and tried the Bioconductor R package ( https://bioconductor.org/packages/release/bioc/html/DRIMSeq.html ) and I think it has great potential.
I was simply wondering whether it was possible to get an estimate for t ...
written 2.5 years ago by
kristoffer.vittingseerup • 20
• updated
2.5 years ago by
Gosia Nowicka • 40
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... The pairwiseAlignment() function have a problematic way of handling empty sequences illustrated by this toy example:
library(Biostrings)
seq1 <- DNAString('ATCG')
seq2 <- DNAString('')
tmp <- pairwiseAlignment(seq1, seq2)
class(tmp)
[1] "PairwiseAlignmentsSingleSubject"
attr(,"package") ...
written 3.1 years ago by
kristoffer.vittingseerup • 20
• updated
18 months ago by
Hervé Pagès ♦♦ 14k
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