User: jsneaththompson

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Posts by jsneaththompson

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Making UpSetR plot with title
... I ended up going with a half-baked solution, although I used GIMP so I could match the font in the UpSetR plot to the title. ...
written 3 days ago by jsneaththompson40
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Comment: C: Making UpSetR plot with title
... It looks like you're right, I'll have to add the title after with some other method ...
written 3 days ago by jsneaththompson40
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Comment: C: Making UpSetR plot with title
... Unfortunately that doesn't work. UpSetR has options for main.bar.color, mainbar.y.label, and mainbar.y.max, so calling main results in `Error in upset(...) argument 7 matches multiple formal arguments` ...
written 3 days ago by jsneaththompson40
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Making UpSetR plot with title
... I'm using UpSetR to create UpSet diagrams [like this][1], but I can't find a way to add a main title to the plot. Does anyone know if this functionality is possible in the UpSetR package at the moment? [1]: http://caleydo.org/assets/images/projects/upset//upsetr-banana.png ...
R upsetr plot written 3 days ago by jsneaththompson40 • updated 3 days ago by dariober8.2k
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Comment: C: Alternatives to Venn Diagrams
... I wasn't aware that UpSet had an R package, I'll look into it, thanks! ...
written 7 days ago by jsneaththompson40
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Alternatives to Venn Diagrams
... I have a spreadsheet with columns representing genes and rows being samples, populated with binary values to indicate the presence of a mutation in a gene for a specific sample. It looks like [this.][1] I've been asked to visualise the intersections for each gene (i.e. IGHV3-23 and TBL1XR1 are both ...
venn plots diagram written 7 days ago by jsneaththompson40 • updated 7 days ago by andrew.j.skelton734.1k
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Using GATK's HaplotypeCaller or Mutect2 for somatic cancer samples with no normal panel
... As the title says, I'm working on variant calling for somatic variant discovery where I have tumour samples, but no normal samples to compare with. Previously I've been using GATK's UnifiedGenotyper for variant calling, but as this tool is deprecated, I want to switch to the newer GATK variant call ...
variant calling gatk somatic variant written 11 days ago by jsneaththompson40 • updated 11 days ago by Sean Davis23k
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Answer: A: Issues installing Pindel from git
... Turned out to be an issue with a recent change to [htslib][1] where hts_drand48() was defined for C, but not for C++. The fix should be implemented in htslib soon, or the ksort.h file in htslib can be altered as shown in the link above. [1]: https://github.com/genome/pindel/issues/76 ...
written 21 days ago by jsneaththompson40
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Issues installing Pindel from git
... I'm currently attempting to install Pindel on my ubuntu machine (16.04 server), but have been having issues with running the ./INSTALL file. The ./INSTALL file takes the path to htslib as an argument, so I also installed htslib from git with git clone https://github.com/samtools/htslib ma ...
software error pindel written 22 days ago by jsneaththompson40
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Minimum base quality for Pindel
... I've been trying to find out whether Pindel has a minimum base quality required for a base to contribute towards a variant call, but I haven't found anything by going through forums or looking at the Pindel user manual. I have been looking at the source code on github and found this section of code ...
variant calling next-gen pindel written 11 weeks ago by jsneaththompson40

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Scholar 21 days ago, created an answer that has been accepted. For A: Issues installing Pindel from git

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