User: kristoffer.vittingseerup

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European Union
Last seen:
4 months ago
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3 years, 8 months ago
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k***********************@bio.ku.dk

Posts by kristoffer.vittingseerup

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Downstream analysis for Salmon output: IsoformSwitchAnalyzeR or TSIS?
... 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 5 months ago by kristoffer.vittingseerup20
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Comment: C: Downstream analysis for Salmon output: IsoformSwitchAnalyzeR or TSIS?
... 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 5 months ago by kristoffer.vittingseerup20
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Comment: C: Systematic underestimation of log2fc values in DESeq?
... 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.  ...
written 14 months ago by kristoffer.vittingseerup20
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Comment: C: Calculating rpkm from counts data?
... How did you quantify the genes (which tool)? And which excat database of gene models did you use for the quantification? ...
written 14 months ago by kristoffer.vittingseerup20
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Comment: C: Updates to BiocStyle formatting
... Awesome job! Are there also updates to "html_vignette" ? ...
written 14 months ago by kristoffer.vittingseerup20
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Answer: A: Calculating rpkm from counts data?
... 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 14 months ago by kristoffer.vittingseerup20
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Comment: C: Usability of ERCC spike-ins in standard RNAseq experiments
... 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 14 months ago by kristoffer.vittingseerup20
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Comment: C: Is it possible to get Isoform-level differential isoform usage form DRIMSeq?
... That sounds extremely usefull - both the feature level test but also the complex designs! Looking forward to try it! ...
written 18 months ago by kristoffer.vittingseerup20
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Is it possible to get Isoform-level differential isoform usage form DRIMSeq?
... 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 ...
splicing drimseq differential isoform usage written 21 months ago by kristoffer.vittingseerup20 • updated 21 months ago by gosia.nowicka30
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Error in pairwiseAlignment when considering an empty seuqnece
... 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") ...
biostrings written 2.4 years ago by kristoffer.vittingseerup20 • updated 9 months ago by Hervé Pagès ♦♦ 13k

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