User: Janet Young
Janet Young • 740
- Reputation:
- 740
- Status:
- Trusted
- Location:
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Website:
- http://research.fhcrc....
- Scholar ID:
- Google Scholar Page
- Last seen:
- 4 days, 11 hours ago
- Joined:
- 12 years, 3 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 - I couldn't quite tell how mature ggbio is. The vignette examples look nice, but I've been finding it a bit challenging to get it to look good with my data. I'm now trying to decide whether to stick to ggbio, or convert to dataframes and use regular ggplots: any thoughts? ...
written 5 days ago by
Janet Young • 740
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... hi all,
I'm exploring ggplot and ggbio - looks like it'll be really useful. But I'm having trouble getting my plots to align on the x axis if one of them has a legend. Is there a way to do make the plots align? or did I accidentally find a bug?
My real example uses the ggbio::plotGrandLinear t ...
written 5 days ago by
Janet Young • 740
• updated
5 days ago by
Michael Lawrence ♦ 11k
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... hi Shian,
I did something similar a few months ago. Herve made a useful function called stackStringsFromGAlignments - I've been using that on each SNP individually (I'm looking at a small genome with not many SNPs, so haven't cared much about efficiency). The details of what I did are a little h ...
written 5 weeks ago by
Janet Young • 740
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... thanks again. that makes sense (the mcols thing).
I'd better steer clear of identical! that's unpredictable and a little scary.
and yes, I'd made a wrong assumption about 'seq' - not sure where that came into my head from that it might be a function to get the seqs. It could have been the 'sho ...
written 5 months ago by
Janet Young • 740
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... Tried stackStringsFromGAlignments - looks great! Thanks again, Herve.
On a quick test it works really well. I did a sanity check with test alignment/region, and I noticed something that I'm sure I can ignore, but wondered if you might care about it for consistency.
I noticed on a test region tha ...
written 5 months ago by
Janet Young • 740
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... (deleted comment - meant to submit it as a reply) ...
written 5 months ago by
Janet Young • 740
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... Wow - so quick! thanks, Herve - really appreciate it.
It's been a while since I've used devel (things are so stable these days), so I'll have to remind myself how to run that, but I'll try this out ASAP.
Janet
...
written 5 months ago by
Janet Young • 740
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... hi there,
It's been a while since I posted - hi all! I miss you bioc people here at the Hutch.
I am wondering whether a function exists that works like stackStringsFromBam, but operates on a GAlignments object (that contains a "seq" column) rather than a bam file. I'm asking because I want to d ...
written 5 months ago by
Janet Young • 740
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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/ ?
...
written 20 months ago by
Janet Young • 740
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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 20 months ago by
Janet Young • 740
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4 months ago,
created a question with more than 1,000 views.
For rtracklayer export: enable trackline for GRanges and RleLists, etc?
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20 months ago,
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For Rgraphviz installation problem
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20 months ago,
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For gviz: controlling track labels
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For problem with cbind on GRanges object - new bug?
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For rtracklayer export: enable trackline for GRanges and RleLists, etc?
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For Rgraphviz installation problem
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For subset a RleList using GRanges object?
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For subset a RleList using GRanges object?
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For subset a RleList using GRanges object?
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For subset a RleList using GRanges object?
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For GenomicRanges request - enable ignore.strand for findOverlaps comparing query with itself?
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For tileGenome for overlapping ranges?
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