User: kristoffer.vittingseerup

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Posts by kristoffer.vittingseerup

<prev • 235 results • page 1 of 24 • next >
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Tools for prediction of protein functionality from AA sequence along
... I have my amino acid sequence of a transcript of interest in bioinformatic tools which can predict different types of annotation and/or functionality based on the sequence alone! Some of the classic would be Pfam and InterScanPro but I'm looking for new ideas :-) Cheers Kristoffer ...
gene assembly rna-seq written 54 minutes ago by kristoffer.vittingseerup1.4k
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Answer: A: Splice site usage from RNA-seq data
... What you are asking is not trivial - and for a very large proportion of genes they will have multiple isoforms which all contribute meaning there will in many cases not be a clear dominant feature. The answer also depends on which organisme you are interested (aka human vs nonhuman) and if you what ...
written 3 days ago by kristoffer.vittingseerup1.4k
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Comment: C: Is there a good way to get the proportions of isoforms *within* a condition usin
... Sure - you would have to use length normalized expression values such as the TPM estimated by Kallisto ...
written 6 days ago by kristoffer.vittingseerup1.4k
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Answer: A: How to quantify mRNA transcripts from RNA-Seq data?
... I wrote a long section about the different things to think about when quantifying RNASeq data (including tools to use) [here][1]. [1]: https://bioconductor.org/packages/devel/bioc/vignettes/IsoformSwitchAnalyzeR/inst/doc/IsoformSwitchAnalyzeR.html#what-quantification-tools-should-i-use ...
written 11 days ago by kristoffer.vittingseerup1.4k
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Comment: C: ANOVA or Linear regression for RNAseq data analysis with 3 factors
... And all of them supports "ANOVA-Style" tests - check the vignettes for the different tools. ...
written 14 days ago by kristoffer.vittingseerup1.4k
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Comment: C: Is there a good way to get the proportions of isoforms *within* a condition usin
... Could you not just for each gene calculate the mean isoform expression over your 3 replicates and then look for which is the largest? ...
written 17 days ago by kristoffer.vittingseerup1.4k
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Comment: C: Tools To Do the Alternative Splicing Analysis
... That seems pretty useful (nice extension of the exon-based approach I described above) - and the differential analysis of both junction and exons uses DEXSeq as the backbone? Does it support counts from other tools than QoRTs? ...
written 19 days ago by kristoffer.vittingseerup1.4k
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Answer: A: Tools To Do the Alternative Splicing Analysis
... Since you posted this with the tag RNA-seq I will assume that you have RNASeq data. Since you mention transcripts I will also assume you have transcript level quantifications (else you can read more about how to obtain such transcript level quantification [here][1].). I will also assume that you hav ...
written 24 days ago by kristoffer.vittingseerup1.4k
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Answer: A: Given a list of cell surface genes, is there a computational possibility to pred
... I do not think so. The best approach I have seen was [this paper][1] whether they use a currated list of receptor-ligant interactions (available [here][2]) and tried using the expression of those pairs. But to my knowledge no computational tool. [1]: https://www.ncbi.nlm.nih.gov/pubmed/30429548 ...
written 24 days ago by kristoffer.vittingseerup1.4k
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Answer: A: Analyzing 3' RNA seq library with DEseq2
... It is quite normal that there is a huge span of expression values - especially on read counts - so you might want to switch to length normalized features (just use the TPM from the Salmon quantification). What you can do is calculate the fraction of the total expression which the top expressed genes ...
written 24 days ago by kristoffer.vittingseerup1.4k

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Scholar 3 days ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
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Scholar 27 days ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
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