User: exin

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exin50
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Posts by exin

<prev • 35 results • page 1 of 4 • next >
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Comment: C: Setting colour palettes correctly for correlation plots
... Looks like what I need... Thank you! I'll look into that. ...
written 11 weeks ago by exin50
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Comment: C: Grouping protein domains into categories?
... Great!! Thank you for these!! ...
written 11 weeks ago by exin50
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Comment: C: Setting colour palettes correctly for correlation plots
... Here we go: cts<- read.table("cor_gene.txt",header=T,row.names=1,sep="\t") cts<- cts[rowSums(cts)>0,] cts$var<- apply(cts, 1, var) ctsv<- cts[cts$var >= quantile(cts$var, c(.95)), ] ctsv$var <- NULL resv<-cor(ctsv,method="pearson") library(" ...
written 11 weeks ago by exin50
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Comment: C: Grouping protein domains into categories?
... Thank you!!! So no way to categorise them other than manually going through the domain names? - Currently they're like zf-C3HC4, zf-C2H2, zf-RING2.... ...
written 11 weeks ago by exin50
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Grouping protein domains into categories?
... I want to compare the domain composition of a few of my cell samples. After mapping peptide sequences on Pfam, I have thousands of domain hits across my dataset. Comparing across my samples hardly makes sense. Are there any references / databases for domain categories? Similar to the clans/ superf ...
domain analysis pfam written 11 weeks ago by exin50 • updated 11 weeks ago by jgreener100
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Setting colour palettes correctly for correlation plots
... Newbie R question: I currently use the standard blue-red palette for plotting a correlation plot: > col<- colorRampPalette(c("blue", "white", "red"))(20) but my data only covers a R value or ~0.2 to 1, hence white is set at ~0.4, which is misleading. How do I select only "some blue and ...
correlation plot R written 11 weeks ago by exin50
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Customised piechart for 2 variables
... I can't quite find the right tool / package to do this, mainly because I'm not sure what it's called. After scRNA-Seq, I have a list of differentially expressed genes (DEGs) in each cell type. I did a Pfam run to scan for all domains in the peptides. Two variables of interest: 1. No. of times a do ...
charts piechart donutchart inforgraphic written 3 months ago by exin50 • updated 3 months ago by ATpoint22k
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Comment: C: Mann-Whitney U test after zero-inflation correction
... Thanks guys!! Yeh there're more replicates. ...
written 4 months ago by exin50
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Mann-Whitney U test after zero-inflation correction
... I'm trying to perform Mann-whitney u test on my data, but realised the excessive zeros cause an issue. I read about the pscl package that uses the zeroinfl function to correct for this, but is unable to find any example online that uses both together. Can I simply perform the test on zeroinfl-corre ...
R written 4 months ago by exin50
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Comment: C: Tool suggestions for bulk domain analyses?
... Oh sweet! Thank you!! :) ...
written 5 months ago by exin50

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