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Thanks for developing a very versatile and user-friendly package. It works very well. Nevertheless, I do have two feature requests / suggestions:
1. In `manhattan()` and `regionplot() `functions, t…
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https://genome.sph.umich.edu/wiki/LocusZoom_Standalone
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Hi,
Do you think it's possible to use the existing `topr` functions to create a colocalization plot? Specifically, multiple locuszoom plots are superimposed on each other with a shared gene track at…
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Hello, I was trying to plot a quick locuszoom plot using some GWAS data and user-provided LD data (formatted per instructions) and when I run the command:
../locuszoom/bin/locuszoom --metal metal_f…
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If I'm reading the code correctly, in order to use my own LD I would need to actually change the source passed to locuszoom.js, find the calls used while populating in locuszoom.js, and then set up ou…
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I have a question, how do you choose the locus for co-localisation when co-locating? The original text says so: "We used default parameters to evaluate colocalization between GWAS signals and the expr…
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So far I've been unable to find recombination rates for GRCh38. May need to liftover the previous GRCh37 rates. The GRCh37 rates currently in locuszoom were generated by lifting over GRCh35:
> Thi…
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Include the UK BioBank GWAS hits across all traits as another catalog, in addition to EBI.
This overlaps with a current task to include these hits in the LocusZoom API, so this is a timely additio…
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Hello,
I have result from META analysis done with METAL and my summary stats looks like this:
SNP BP CHR A1 A2 Weight Z P Direction
rs11693919 127673527 2 C T 19586 -5.565 2.617e-08 ---
rs1020…
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Hello,
I believe that there is a bug in Locuszoom version 1.4 ("05/01/2017").
If no SNP is specified, and the region is specified using the chr/start/end, then the region is now defined as 'chr16:69…