User: Janet Young

gravatar for Janet Young
Janet Young740
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

<prev • 118 results • page 1 of 12 • next >
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Comment: C: ggbio tracks not aligned when legend present in one track
... 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 Young740
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ggbio tracks not aligned when legend present in one track
... 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 ...
ggbio written 5 days ago by Janet Young740 • updated 5 days ago by Michael Lawrence11k
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Answer: A: How to query a base along an aligned read by genomic position?
... 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 Young740
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Comment: C: stackStringsFromBam equivalent for GAlignments with seq
... 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 Young740
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Answer: A: stackStringsFromBam equivalent for GAlignments with seq
... 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 Young740
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Comment: C: stackStringsFromBam equivalent for GAlignments with seq
... (deleted comment - meant to submit it as a reply) ...
written 5 months ago by Janet Young740
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Answer: A: stackStringsFromBam equivalent for GAlignments with seq
... 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 Young740
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stackStringsFromBam equivalent for GAlignments with seq
... 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 ...
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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 20 months ago by Janet Young740
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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 20 months ago by Janet Young740

Latest awards to Janet Young

Popular Question 4 months ago, created a question with more than 1,000 views. For rtracklayer export: enable trackline for GRanges and RleLists, etc?
Popular Question 20 months ago, created a question with more than 1,000 views. For Rgraphviz installation problem
Popular Question 20 months ago, created a question with more than 1,000 views. For gviz: controlling track labels
Popular Question 20 months ago, created a question with more than 1,000 views. For problem with cbind on GRanges object - new bug?
Popular Question 20 months ago, created a question with more than 1,000 views. For rtracklayer export: enable trackline for GRanges and RleLists, etc?
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Rgraphviz installation problem
Popular Question 2.6 years ago, created a question with more than 1,000 views. For subset a RleList using GRanges object?
Popular Question 2.6 years ago, created a question with more than 1,000 views. For subset a RleList using GRanges object?
Popular Question 2.6 years ago, created a question with more than 1,000 views. For subset a RleList using GRanges object?
Popular Question 3.3 years ago, created a question with more than 1,000 views. For subset a RleList using GRanges object?
Centurion 4.1 years ago, created 100 posts.
Student 4.3 years ago, asked a question with at least 3 up-votes. For tileGenome for overlapping ranges?
Autobiographer 5.2 years ago, has more than 80 characters in the information field of the user's profile.

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