User: Janet Young
Janet Young • 730
- Reputation:
- 730
- Status:
- Trusted
- Location:
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Website:
- http://research.fhcrc....
- Scholar ID:
- Google Scholar Page
- Last seen:
- 1 week, 3 days ago
- Joined:
- 10 years, 7 months ago
- Email:
- j******@fhcrc.org
I provide bioinformatics support to members of Harmit Malik's lab. We work on a number of evolutionary questions using diverse tools.
Posts by Janet Young
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... Thanks, Michael - appreciate it. Yes, I'll start using github instead for stuff like this.
Maybe the github pages are worth a mention on http://www.bioconductor.org/help/support/posting-guide/ ?
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written 10 days ago by
Janet Young • 730
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... Hi there,
I'm using rtracklayer's export function to get a bed file, and then I upload that file manually to the UCSC genome browser via my web browser.
I am using the trackLine/colorByStrand function - it seems to be almost working fine, but not quite. It would be great if the colorByStrand opti ...
written 11 days ago by
Janet Young • 730
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... done (https://github.com/Bioconductor/ensemblVEP/issues/2). thanks again!
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written 5 weeks ago by
Janet Young • 730
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... Thanks, Lori - that did let me troubleshoot successfully. I did just put in a github issue with a request to see the system call - that was really useful once you showed me how to do it using debugonce.
I should probably update to VEP v90 soon, but perhaps it's also useful to let you know where I s ...
written 5 weeks ago by
Janet Young • 730
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... Hi there,
This page - http://www.bioconductor.org/packages/release/bioc/html/ensemblVEP.html - says that the EnsemblVEP bioconductor package needs v88 of the Ensembl API, but from some of the help pages within ensemblVEP v1.20.0 it looks like maybe v90 is now supported too?
I'm asking because ...
written 5 weeks ago by
Janet Young • 730
• updated 5 weeks ago by
shepherl ♦♦ 560
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... Thanks, Jianhong - I appreciate it
...
written 9 weeks ago by
Janet Young • 730
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... Hi there,
I'm just starting to explore the ChIPpeakAnno package - it looks really useful: thank you for creating it. I'm following some of the vignettes and using assignChromosomeRegion to get a first glimpse of where our peaks tend to map: that works well. What I'd love to do is to see how diff ...
written 9 weeks ago by
Janet Young • 730
• updated 9 weeks ago by
Julie Zhu • 3.8k
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... Hi there,
I'm using binnedAverage, and would love to see an na.rm option added if possible. I do have a hacked version of binnedAverage that I can use instead, but thought I'd suggest adding na.rm as an enhancement for the existing function.
My motivation is that I have a set of SNP genotype fre ...
written 11 months ago by
Janet Young • 730
• updated 11 months ago by
Hervé Pagès ♦♦ 13k
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... Thanks again - that is fairly close. I have enough samples (2 groups, 4 samples each) that it'd look better to mimic the horizon type multipanel grouped plot rather than than the overlaid histograms. I can get something pretty close to what I want just by plotting coverage as separate individual ...
written 20 months ago by
Janet Young • 730
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... Thanks again, Florian - that's helpful.
Here's a suggestion for a future enhancement: would it be easy for you to implement a plot type for DataTrack that mimics the coverage track for AlignmentTrack plots? I love the look of the filled gray polygon, rather than the simple line-only plot that ty ...
written 20 months ago by
Janet Young • 730
Latest awards to Janet Young
Popular Question
11 months ago,
created a question with more than 1,000 views.
For subset a RleList using GRanges object?
Popular Question
11 months ago,
created a question with more than 1,000 views.
For subset a RleList using GRanges object?
Popular Question
20 months ago,
created a question with more than 1,000 views.
For GenomicRanges request - enable ignore.strand for findOverlaps comparing query with itself?
Popular Question
20 months ago,
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For subset a RleList using GRanges object?
Centurion
2.5 years ago,
created 100 posts.
Student
2.7 years ago,
asked a question with at least 3 up-votes.
For tileGenome for overlapping ranges?
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