How to Get the Protein Sequence in R like the lolliplot from cBioportal

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3.0 years ago

Lesdormis • 0

Dear Biostars community,

I am working on multiple lolliplots like the one in cBioportal enter image description here

I am wondering is that a package or a way in R that can let you get access the information like the length of amino acid and domain regions of your input protein? So that I can generate a lolliplot like this by trackViewer or ggplot for my interesting gene list.

I know you can get these information from queries like NCBI or Uniport, But I need a more efficient way for doing that.

Thanks!

cBioportal R protein • 1.2k views

ADD COMMENT • link 3.0 years ago by Lesdormis • 0

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https://bioconductor.org/packages/release/bioc/vignettes/trackViewer/inst/doc/lollipopPlot.html

https://github.com/joiningdata/lollipops

Please use google.

ADD REPLY • link 3.0 years ago by cpad0112 21k

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yes, thanks. But I already knew trackViewer. I was wondering how to get the GRanges object of a protein so that I can input to trackViewer. And for your second link, it looks very good. But I cannot implement into my R pipeline. Thanks anyway

ADD REPLY • link 3.0 years ago by Lesdormis • 0

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