User: User000
User000 • 240
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Posts by User000
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... Hi,
Does anybody know of any database where I can find cloned genes of plants? Otherwise, if I have gene symbols where to get the fasta sequences?
Thanks! ...
written 10 days ago by
User000 • 240
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C: Add a legend to circos plot
... thanks a lot, yes i have seen inkscape before, seems to be confusing. Would you mind to explain shortly how to use it? I might try GIMP as well if it works.. ...
written 9 weeks ago by
User000 • 240
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... Hello,
I would like to add A,B,C tracks labelling to a circos plot. Would you suggest how to do it? I already left a space between the chromosomes. ...
written 9 weeks ago by
User000 • 240
• updated
9 weeks ago by
Ibrahim Tanyalcin • 820
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C: Download genes from KEGG pathway
... thanks a lot! i will have a look! ...
written 10 weeks ago by
User000 • 240
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C: Download genes from KEGG pathway
... thank you, I have KGML files, but I am interested in having the seq-s...how can I download them? (not 1 by 1..) ...
written 10 weeks ago by
User000 • 240
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... Hello,
I am would like to download all genes of i.e. arabidopsis thaliana from i.e. circadian rhythm pathway in fasta format. Is there a way to download them in a batch mode, instead of opening and saving every single gene in a fasta format? ...
written 11 weeks ago by
User000 • 240
• updated
11 weeks ago by
theobroma22 • 930
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... Hi,
I was using MUMmer to make a dot plot of several genes. However, I was wondering if there is a way to make a dot plot of multiple genes in R? i.e, I want to make dot plot of multiple genes for each chromosome in one graph.
EDIT: Apart from fasta seq-s I also have the gene start-end information ...
written 3 months ago by
User000 • 240
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... yes, see the question I asked time ago: https://www.biostars.org/p/243695/#244051 ...
written 3 months ago by
User000 • 240
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... yes, I did. I used Deseq2, see the link: http://www-huber.embl.de/users/klaus/Teaching/DESeq2Predoc2014.html#quality-control-and-normalization-of-the-count-data ...
written 3 months ago by
User000 • 240
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... Hi,
I was new to R as well when I had to do similar analysis, so I spent several days searching and trying to get what I need, because there is a lot of info on this.
This is the PCA function I used after normalization step.
## Modified plotPCA from DESeq2 package.
plotPCA.san <- funct ...
written 3 months ago by
User000 • 240
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