User: Janet Young

gravatar for Janet Young
Janet Young730
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, 3 weeks ago
Joined:
12 years, 1 month 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 • 115 results • page 1 of 12 • next >
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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 3 months ago by Janet Young730
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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 3 months ago by Janet Young730
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Comment: C: stackStringsFromBam equivalent for GAlignments with seq
... (deleted comment - meant to submit it as a reply) ...
written 3 months ago by Janet Young730
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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 3 months ago by Janet Young730
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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 18 months ago by Janet Young730
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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 18 months ago by Janet Young730
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Comment: C: ensemblVEP supported versions, and troubleshooting
... done (https://github.com/Bioconductor/ensemblVEP/issues/2). thanks again! ...
written 19 months ago by Janet Young730
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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 19 months ago by Janet Young730
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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 19 months ago by Janet Young730 • updated 19 months ago by shepherl ♦♦ 1.6k

Latest awards to Janet Young

Popular Question 12 weeks ago, created a question with more than 1,000 views. For rtracklayer export: enable trackline for GRanges and RleLists, etc?
Popular Question 18 months ago, created a question with more than 1,000 views. For Rgraphviz installation problem
Popular Question 18 months ago, created a question with more than 1,000 views. For gviz: controlling track labels
Popular Question 18 months ago, created a question with more than 1,000 views. For problem with cbind on GRanges object - new bug?
Popular Question 18 months ago, created a question with more than 1,000 views. For rtracklayer export: enable trackline for GRanges and RleLists, etc?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Rgraphviz installation problem
Popular Question 2.4 years ago, created a question with more than 1,000 views. For subset a RleList using GRanges object?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For subset a RleList using GRanges object?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For subset a RleList using GRanges object?
Popular Question 3.2 years ago, created a question with more than 1,000 views. For subset a RleList using GRanges object?
Centurion 4.0 years ago, created 100 posts.
Student 4.2 years ago, asked a question with at least 3 up-votes. For tileGenome for overlapping ranges?
Autobiographer 5.1 years ago, has more than 80 characters in the information field of the user's profile.

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