User: kristoffer.vittingseerup

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@kvittingseerup
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4 years, 11 months ago
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k***********************@bio.ku.dk

Posts by kristoffer.vittingseerup

<prev • 443 results • page 2 of 45 • next >
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Answer: A: Calculating differential expression genes between two sample sequenced using 10x
... Taking the time out to follow the Seurat tutorial is worth it. Single cell data have so many biases and problems you will need to have under control for your differential expression analysis to be trustworthy. With regards to your data I would recommend using Seurat3's data integration to create a ...
written 5 weeks ago by kristoffer.vittingseerup3.0k
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Answer: A: How to compare two sets of results from Limma?
... I would start by comparing the log2FC of all genes analyzed between the two studies - it might be that some genes are not DE in one study but the log2FC are similar.. One way to do this would be to plot the log2FC vs each other colouring by the DE status of in the two models. You can also do this on ...
written 6 weeks ago by kristoffer.vittingseerup3.0k
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Comment: C: deleting TCGA replicated samples
... Please update your question with code instead of supplying it as a answer. Also use the propper formatting of code instead of pasting it to ensure readability. ...
written 6 weeks ago by kristoffer.vittingseerup3.0k
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Comment: C: deleting TCGA replicated samples
... Specifically what data are you working on? Where do you get the data from? Could you post an example of a duplicated sample id? ...
written 6 weeks ago by kristoffer.vittingseerup3.0k
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Comment: C: OUTRIDER for gene expression outliers (could not find function "OutriderDataSet"
... Did you get any warnings when loading the OUTRIDER library? ...
written 9 weeks ago by kristoffer.vittingseerup3.0k
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Answer: A: The best tool for time course differential expression with R
... Appart from ATpoint's suggestion I can recommend [voom-limma][1] IF you have many timepoints since they allow for modeling via splines. You can take a look in section 9.6 (p 47) of the [limma vignette][2] (9.6.2 for the spline modeling). [1]: https://bioconductor.org/packages/release/bioc/html/l ...
written 9 weeks ago by kristoffer.vittingseerup3.0k
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Comment: C: Definition of an isoform switching?
... Just a small addition: As well as alternative splicing isoform switches is also the result of alternative transcription start and termination sites - and the changes can be quite large. ...
written 10 weeks ago by kristoffer.vittingseerup3.0k
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Comment: C: Differential expression tool that can take TPM as input?
... the length normalisation does not make to much of a difference as it is hopefully the same in all samples - and you only compare the sample gene between samples. Meaning the results you got for CPM should be usefull. ...
written 10 weeks ago by kristoffer.vittingseerup3.0k
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Comment: C: Definition of an isoform switching?
... Great answer (I have to say that since I'm the author of the refrence :D). Just want to add that the more I work with this field the more I find that isoform switches occurs in all biological systems/comparisons. Compare different tissues or cell types - then they use different isoforms, compare dif ...
written 10 weeks ago by kristoffer.vittingseerup3.0k
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Comment: C: Bioinformatics vs. the Climate Crisis
... No climate crisis - you are kidding right? https://www.un.org/en/sections/issues-depth/climate-change/ ...
written 11 weeks ago by kristoffer.vittingseerup3.0k

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Scholar 11 weeks ago, created an answer that has been accepted. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: RNA-seq analysis between 2 closely related strains of the same species
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Tools To Do the Alternative Splicing Analysis
Scholar 3 months ago, created an answer that has been accepted. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
Teacher 3 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
Teacher 3 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
Scholar 3 months ago, created an answer that has been accepted. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
Teacher 3 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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Scholar 4 months ago, created an answer that has been accepted. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
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Teacher 5 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
Scholar 5 months ago, created an answer that has been accepted. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
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Teacher 6 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
Scholar 6 months ago, created an answer that has been accepted. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
Scholar 7 months ago, created an answer that has been accepted. For A: which option is better for DESeq2 analysis: salmon or htseq-count?

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