User: kristoffer.vittingseerup

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Posts by kristoffer.vittingseerup

<prev • 89 results • page 1 of 9 • next >
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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 13 days 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 17 days ago by kristoffer.vittingseerup470 • updated 16 days ago by toralmanvar290
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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 weeks ago by kristoffer.vittingseerup470
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Answer: A: what are gene ratio and bg ratio in differentially expressed gene enrichment ana
... You need to look for the enrichment score typically given as an odds ratio. And naturally you also need to consider the statistical test. If you want more help you need to upload an example of the result (and more info on how you did the analysis - which webside/tool did you use etc) ...
written 4 weeks ago by kristoffer.vittingseerup470
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Answer: A: Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
... I just pushed an update of my R package [IsoformSwitchAnalyzeR][1] to Bioconductor which introduces a module for alternative splicing. For individual splice sites the already suggested tools might be better - but for a genome wide analysis of splicing it is very convenient to frame it as a compari ...
written 6 weeks ago by kristoffer.vittingseerup470
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Answer: A: Any Promising Addition to Alternative Splicing Detection tools for Rna-Seq Data
... I just pushed an update of my R package [IsoformSwitchAnalyzeR][1] to Bioconductor which introduces a module for alternative splicing. For individual splice sites the already suggested tools are probably better - but for a genome wide analysis of splicing it is very convenient to frame it as a com ...
written 6 weeks ago by kristoffer.vittingseerup470
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Answer: A: Summary of alternative splicing from Cufflinks
... I just pushed an update of my R package [IsoformSwitchAnalyzeR][1] to Bioconductor which introduces a module for alternative splicing. It directly supports import of Cufflinks/Cuffdiff data and allows for both visualisation of individual genes (see example [here][2]) as well as genome wide summar ...
written 6 weeks ago by kristoffer.vittingseerup470
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Answer: A: How does Cufflinks DE calculate q-value?
... That would be very hard - Cufflinks/Cuffdiff uses a quite advanced statistical model. For more information take a look at this [article][1] - the supplementary methods contains the mathematical description of the model. There are other better methods if you only have FPKM values, but do you have ac ...
written 6 weeks ago by kristoffer.vittingseerup470
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Answer: A: workflow/tool for alternative splicing
... I just pushed an update of my R package [IsoformSwitchAnalyzeR to Bioconductor][1] which introduces a module for alternative splicing. For individual splice sites the already suggested tools are probably better - but for a genome wide analysis of splicing it is very convenient to frame it as a compa ...
written 6 weeks ago by kristoffer.vittingseerup470
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Comment: C: kallisto/sleuth for single sample pathway enrichment
... You should not aggregate gene to pathway levels (that does not work since a gene is part of many pathways) instead you should use gene-set analysis tools. The easiest to use in R is probably [gProfileR][1] [1]: https://cran.r-project.org/web/packages/gProfileR/index.html ...
written 12 weeks ago by kristoffer.vittingseerup470

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Teacher 13 days ago, created an answer with at least 3 up-votes. For A: RNA-seq analysis between 2 closely related strains of the same species
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Scholar 7 months ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
Scholar 8 months ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
Scholar 10 months ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: RNA-seq analysis between 2 closely related strains of the same species

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