User: kristoffer.vittingseerup

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European Union
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3 years, 5 months ago
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Posts by kristoffer.vittingseerup

<prev • 96 results • page 1 of 10 • next >
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Comment: C: What information in dispersion plot using edgeR?
... I do feel we need to mention that although limma was originally made for microarrays it continues to be amongst the top tools in benchmarks of DE analysis on RNAseq data - especially when using voom to add weights to the data. ...
written 8 weeks ago by kristoffer.vittingseerup470
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Comment: C: GREIN: An interactive web platform for re-processing and re-analyzing GEO RNA-se
... That's really cool! What about transcript level abundances? Those would often be nicer to have as they are corrected for all the biases... ...
written 9 weeks ago by kristoffer.vittingseerup470
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Comment: C: GREIN: An interactive web platform for re-processing and re-analyzing GEO RNA-se
... Looks very usefull - thanks for sharing! I have two questions: 1) Are transcript level estimats available? 2) Why is amongst others GSE26024 not in there? ...
written 10 weeks ago by kristoffer.vittingseerup470
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Answer: A: How to know favorite and unfavorite for survival analysis programmly?
... I recomend useing [R's survival package][1] more specifically the [cox regression][2]. If you do that coefficient will be the hazard ratio where larger than 1 means worse outcome. [1]: https://cran.r-project.org/web/packages/survival/index.html [2]: https://cran.r-project.org/web/packages/survi ...
written 10 weeks ago by kristoffer.vittingseerup470
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Comment: C: question on sequencing strategies and batch effects
... Please make your own seperate question instead of writing in another question. ...
written 10 weeks ago by kristoffer.vittingseerup470
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Answer: A: Run htseq-count with multiple sam files?
... Why not quantify with [Salmon][1] - will give you much better gene level estimats (according to amongst other [this][2]) [1]: https://github.com/COMBINE-lab/salmon [2]: https://cgatoxford.wordpress.com/2016/08/17/why-you-should-stop-using-featurecounts-htseq-or-cufflinks2-and-start-using-kalli ...
written 10 weeks ago by kristoffer.vittingseerup470
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Answer: A: Error for reading .gtf file in R
... Try rtracklayer::import() ...
written 12 weeks ago by kristoffer.vittingseerup470
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Comment: C: Any RNASeq dataset with large number of replicates out there?
... That seems to be just one chromosome (chr X)? ...
written 3 months ago by kristoffer.vittingseerup470
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Any RNASeq dataset with large number of replicates out there?
... Does anyone know of an RNAseq dataset with a large number (min 5-10) of replicate - like the [Bottomly et al 2011 dataset][1] but with paired-end reads? Cheers Kristoffer [1]: https://www.ncbi.nlm.nih.gov//pubmed/21455293 ...
dataset rna-seq written 3 months ago by kristoffer.vittingseerup470 • updated 3 months ago by toralmanvar510
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Answer: A: Alternative splicing analysis following kallisto?
... Hi Dina Take a look at my R package [IsoformSwitchAnalyzeR][1] (you need version 1.1.07 or higher) - it directly supports Kallisto data and can analyze alternative splicing both individual genes as well as genome wide level. See examples for individual genes (isoform switch) [here][2] or for the gl ...
written 4 months ago by kristoffer.vittingseerup470

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