User: Janet Young

gravatar for 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:
10 years, 9 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

<prev • 110 results • page 1 of 11 • next >
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Answer: A: rtracklayer colorByStrand - is it possible to add quotes?
... 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/  ?          ...
written 10 weeks ago by Janet Young • 730
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rtracklayer colorByStrand - is it possible to add quotes?
... 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 ...
rtracklayer written 10 weeks ago by Janet Young • 730
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Comment: C: ensemblVEP supported versions, and troubleshooting
... done (https://github.com/Bioconductor/ensemblVEP/issues/2). thanks again! ...
written 3 months ago by Janet Young • 730
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Comment: C: ensemblVEP supported versions, and troubleshooting
... 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 3 months ago by Janet Young • 730
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ensemblVEP supported versions, and troubleshooting
... 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 ...
ensemblvep written 3 months ago by Janet Young • 730 • updated 3 months ago by shepherl ♦♦ 620
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Answer: A: integer overflow in ChIPpeakAnno assignChromosomeRegion
... Thanks, Jianhong - I appreciate it ...
written 4 months ago by Janet Young • 730
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integer overflow in ChIPpeakAnno assignChromosomeRegion
... 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 ...
chippeakanno assignchromosomeregion written 4 months ago by Janet Young • 730 • updated 4 months ago by Julie Zhu • 3.8k
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binnedaverage - is it possible to add an na.rm option?
... 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 ...
genomicranges written 13 months ago by Janet Young • 730 • updated 13 months ago by Hervé Pagès ♦♦ 13k
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Answer: A: gviz: controlling track labels
... 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 22 months ago by Janet Young • 730
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Answer: A: gviz: controlling track labels
... 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 22 months ago by Janet Young • 730

Latest awards to Janet Young

Popular Question 13 months ago, created a question with more than 1,000 views. For subset a RleList using GRanges object?
Popular Question 13 months ago, created a question with more than 1,000 views. For Rgraphviz installation problem
Popular Question 13 months ago, created a question with more than 1,000 views. For subset a RleList using GRanges object?
Popular Question 13 months ago, created a question with more than 1,000 views. For subset a RleList using GRanges object?
Popular Question 22 months ago, created a question with more than 1,000 views. For subset a RleList using GRanges object?
Popular Question 22 months ago, created a question with more than 1,000 views. For GenomicRanges request - enable ignore.strand for findOverlaps comparing query with itself?
Centurion 2.6 years ago, created 100 posts.
Student 2.9 years ago, asked a question with at least 3 up-votes. For tileGenome for overlapping ranges?
Autobiographer 3.8 years ago, has more than 80 characters in the information field of the user's profile.
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