User: kristoffer.vittingseerup

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@kvittingseerup
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Posts by kristoffer.vittingseerup

<prev • 435 results • page 1 of 44 • next >
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Answer: A: Learning RNASeq Analysis using my own DATA that needs to be analyzed
... For an overview the different ways to analyze your data you can refere to [this][4]. With regards to gene DE analysis there are two major ways you can go: Option 1) I just want to get this done asap. There are many possibilities but you can use a tool like [3D RNA-seq][1] or [Galaxy][2] Option 2) ...
written 4 hours ago by kristoffer.vittingseerup3.0k
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Comment: C: Calculating differential expression genes between two sample sequenced using 10x
... You can use Seurat's Read10X() function to get the 10X data into R. It is true you might want to extend the processing part in the link above with the standard processing and QC from this [vignette][1]. If that was not what you meant could you be a bit more specific about what your problem is? [ ...
written 7 days ago by kristoffer.vittingseerup3.0k
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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 11 days 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 12 days 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 14 days 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 17 days 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 5 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 5 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 6 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 6 weeks ago by kristoffer.vittingseerup3.0k

Latest awards to kristoffer.vittingseerup

Scholar 11 days ago, created an answer that has been accepted. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
Scholar 5 weeks ago, created an answer that has been accepted. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
Teacher 5 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
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: Bioinformatics vs. the Climate Crisis
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Scholar 7 weeks ago, created an answer that has been accepted. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
Teacher 7 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 9 weeks ago, created an answer that was upvoted at least 5 times. For A: Tools To Do the Alternative Splicing Analysis
Scholar 10 weeks ago, created an answer that has been accepted. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
Teacher 10 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
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
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 12 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
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?
Scholar 3 months ago, created an answer that has been accepted. For A: Error while loading the data structrure in the ballgown tool
Teacher 4 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 4 months ago, created an answer that has been accepted. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
Student 4 months ago, asked a question with at least 3 up-votes. For Equivavalent of rlog() or vst() for abundance values
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?
Scholar 6 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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