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GMOD / JBrowseR

R interface to the JBrowse 2 Linear Genome View.
https://gmod.github.io/JBrowseR/
Apache License 2.0
35 stars 3 forks source link

Suggestions on JBrowseR #13

Closed zhanxw closed 2 years ago

zhanxw commented 3 years ago

JBrowseR is very useful. However, I want to suggest two features:

  1. tracks(...) needs to detect name collision. For example, when I add two VCF tracks, abc.prog1.vcf.gz and abc.prog2.vcf.gz, both will have the name values abc. Then the browser will not render either file correctly.
  2. search by gene names. currently, users can specify genomic location, but cannot search specific gene names. JBrowse CLI seems to support it (link: https://jbrowse.org/jb2/docs/combined/#indexing-feature-names-for-searching), but JBrowseR does not seem to support it now.
elliothershberg commented 2 years ago

Hey @zhanxw , thanks for both suggestions. We can work on incorporating these features.

Spartanzhao commented 2 years ago

Honestly, I think this tool is much worse that other tools that have been published, it's really hard to use, and I got lots of errors during installation. It's really useless to me.

cmdcolin commented 2 years ago

@Spartanzhao if you are interested in describing what errors you got, we can try to help. please avoid venting your frustrations like this though, it's not kind or helpful

elliothershberg commented 2 years ago

@cmdcolin this person just had a paper rejected in JOSS that I was a reviewer on. I think he's a bit upset about that.

It has reminded me, I need to find time this weekend to update JB2 in this package! 😄

elliothershberg commented 2 years ago

A new release is on its way to CRAN with a new function text_index() supporting gene name search.

Check out example_apps/hg38_index_app.R for example usage!

While it may be worth avoiding name collisions down the road, I haven't implemented this feature yet—it's probably best to avoid data files with duplicate names.