Moderator: Nicolas Rosewick

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Posts by Nicolas Rosewick

<prev • 919 results • page 1 of 92 • next >
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Comment: C: How to remove outliers using PCA in R?
... I guess in the `pca` object you should have `PC1` and `PC2` (information used to plot). Use these to filter out the samples i.e. `PC1 < -100` ...
written 6 hours ago by Nicolas Rosewick7.9k
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Comment: C: How to remove outliers using PCA in R?
... Are all samples from the same dataset ? Do you have metadata on this samples (sequencing kit ? type ? cell type ? sequencing plateform, etc...) IMO you see here a clear (non-biological) batch effect ...
written 6 hours ago by Nicolas Rosewick7.9k
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Comment: C: How to remove outliers using PCA in R?
... You should explain how you generated your PCA plot (from which type of data ? ). Put your code. And a minimal reproducible example. ...
written 7 hours ago by Nicolas Rosewick7.9k
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Answer: A: Correlation test for multiple variables and adjusted p values
... You should use all pvalues for multi testing correction One good idea is to plot nominal pvalues and check the shape of the distribution . Check here for explanation: http://varianceexplained.org/statistics/interpreting-pvalue-histogram/ ...
written 1 day ago by Nicolas Rosewick7.9k
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Answer: A: Evolutionary distance from as many organisms as possible to humans
... With EMBL Interactive Tree of Life you can export in various text format (e.g. : phyloXML) : https://itol.embl.de/itol.cgi ...
written 7 days ago by Nicolas Rosewick7.9k
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Answer: A: Filtering 2-fold differentially expressed genes
... You should use limma to compute gene expression statistics (p-value, foldchange) and use this value to filter out your data. https://bioconductor.org/packages/release/bioc/html/limma.html Otherwise you can do something like this : # control_samples # vector of control sample names # treat ...
written 22 days ago by Nicolas Rosewick7.9k
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Number of samples with rare mutation per gene in gnomAD
... HI, I would like to know if there is a way to know how many samples are mutated per gene in gnomAD. Let me explain : In gnomAD vcf you can see the variants an their associated allele frequency in the population. I already filter the vcf based on AF to only get rare mutation with a high VEP impact. ...
mutation gnomad written 25 days ago by Nicolas Rosewick7.9k
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Answer: A: Struggling to use the GATK HaplotypeCaller on my bam files.
... In the GATK folder you should have an executable file named gatk you should add it to your PATH or create a variable in your script storing the path to this file : gatk="path/to/the/file/gatk" genome="path/to/genome/file/" # fasta file used to align the data e.g. hg38 for human interv ...
written 26 days ago by Nicolas Rosewick7.9k • updated 26 days ago by WouterDeCoster40k
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Comment: C: How to predict sample ethnicty from a VCF using 1000G or gnomAD ?
... Thank you @WouterDeCoster . Exactly what I wanted :) ...
written 26 days ago by Nicolas Rosewick7.9k
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How to predict sample ethnicty from a VCF using 1000G or gnomAD ?
... Hi, There were already some discussion started to predict sample ethnicity from population genetic studies (1000G, gnomAD) e.g. https://www.biostars.org/p/300930/#300933 who used the PC from 1000G to create a predicitve model. However I was wondering if there are already tools/R packages that take ...
vcf 1000g ethnicity snp gnomad written 26 days ago by Nicolas Rosewick7.9k • updated 26 days ago by WouterDeCoster40k

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Scholar 7 days ago, created an answer that has been accepted. For C: How to increase cytoscape memory?
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Scholar 22 days ago, created an answer that has been accepted. For C: How to increase cytoscape memory?
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