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:
- 2 months, 2 weeks ago
- Joined:
- 11 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 12 months 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 12 months ago by
Janet Young • 730
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... done (https://github.com/Bioconductor/ensemblVEP/issues/2). thanks again!
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written 13 months 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 13 months 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 13 months ago by
Janet Young • 730
• updated
13 months ago by
shepherl ♦♦ 1.3k
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... Thanks, Jianhong - I appreciate it
...
written 14 months 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 14 months ago by
Janet Young • 730
• updated
14 months ago by
Julie Zhu • 4.0k
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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 23 months ago by
Janet Young • 730
• updated
23 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 2.7 years 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 2.7 years ago by
Janet Young • 730
Latest awards to Janet Young
Popular Question
12 months ago,
created a question with more than 1,000 views.
For Rgraphviz installation problem
Popular Question
12 months ago,
created a question with more than 1,000 views.
For gviz: controlling track labels
Popular Question
12 months ago,
created a question with more than 1,000 views.
For problem with cbind on GRanges object - new bug?
Popular Question
12 months ago,
created a question with more than 1,000 views.
For rtracklayer export: enable trackline for GRanges and RleLists, etc?
Popular Question
23 months ago,
created a question with more than 1,000 views.
For subset a RleList using GRanges object?
Popular Question
23 months ago,
created a question with more than 1,000 views.
For Rgraphviz installation problem
Popular Question
23 months ago,
created a question with more than 1,000 views.
For subset a RleList using GRanges object?
Popular Question
23 months ago,
created a question with more than 1,000 views.
For subset a RleList using GRanges object?
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For subset a RleList using GRanges object?
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For GenomicRanges request - enable ignore.strand for findOverlaps comparing query with itself?
Centurion
3.5 years ago,
created 100 posts.
Student
3.7 years ago,
asked a question with at least 3 up-votes.
For tileGenome for overlapping ranges?
Autobiographer
4.6 years ago,
has more than 80 characters in the information field of the user's profile.
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