User: stianlagstad

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stianlagstad90
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Posts by stianlagstad

<prev • 64 results • page 1 of 7 • next >
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Comment: C: Gviz: Help figuring out `arguments imply differing number of rows: 0, 1` error
... Thank you! :) ...
written 9 months ago by stianlagstad90
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Comment: C: Gviz: Help figuring out `arguments imply differing number of rows: 0, 1` error
... Thank you! :) ...
written 9 months ago by stianlagstad90
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Gviz: Help figuring out `arguments imply differing number of rows: 0, 1` error
... Hi, I'm running into an error that I haven't been able to get around. Here's the code needed to reproduce it (the data is available here): source("https://bioconductor.org/biocLite.R") biocLite("chimeraviz") library(chimeraviz) fc <- importFusioncatcher(filename = 'SRR1559032_out/final-list_ ...
gviz written 9 months ago by stianlagstad90 • updated 9 months ago by Robert Ivanek530
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Gviz: Possible 5' and 3' marker errors
... This code: ``` transcriptID <- "ENST00000395443" mart <- biomaRt::useMart(   biomart = "ENSEMBL_MART_ENSEMBL",   dataset = "hsapiens_gene_ensembl",   host = "dec2013.archive.ensembl.org") # Create transcript track biomartTrack <- Gviz::BiomartGeneRegionTrack(   filters = list(     ensembl ...
software error written 11 months ago by stianlagstad90
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Comment: C: chimeraviz - import own fusion file for visualization
... No problem! Just ask more here or create an issue in the github repository if there's anything else. ...
written 14 months ago by stianlagstad90
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Answer: A: chimeraviz - import own fusion file for visualization
... Thank you for your interest in using chimeraviz!:) You can use your own file with the import functions like this: # Load chimeraviz library(chimeraviz) # A reference to your fusion file myfile <- "/home/stian/dev/soapfuse_833ke_final.Fusion.specific.for.genes" fusions <- importSoapfuse(myfil ...
written 14 months ago by stianlagstad90
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Comment: C: Gviz/Biostrings memory issue?
... Alright. Thanks again! ...
written 22 months ago by stianlagstad90
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Comment: C: Gviz/Biostrings memory issue?
... I was hoping something could be done about that, since I'm not interested in showing the reads. Could it not be possible to count the coverage without holding everything in memory? ...
written 22 months ago by stianlagstad90
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Comment: C: Gviz/Biostrings memory issue?
... Thank you for responding. I'm saying that when I run plotTracks like in my post, my R session stops responding because it is demanding too much memory. The only way out is to shut down the program (killall rstudio). Were you abel to produce the plot I tried to plot? ...
written 22 months ago by stianlagstad90
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Gviz/Biostrings memory issue?
... I'm running into memory issues trying to plot a region from a .BAM file produced from RACE-seq. The .BAM file is not huge, but the high coverage might be the problem. Here's an example: # Reproducing the memory problem # First, source this alternative bam-file import function for use with Gviz::Al ...
biostrings gviz written 22 months ago by stianlagstad90

Latest awards to stianlagstad

Popular Question 17 months ago, created a question with more than 1,000 views. For Gviz: How to color parts of transcript in BiomartGeneRegionTrack?
Supporter 2.4 years ago, voted at least 25 times.
Scholar 2.5 years ago, created an answer that has been accepted. For A: Gviz: Given transcript names and TxDb, how do you plot grouped transcripts?
Scholar 2.5 years ago, created an answer that has been accepted. For A: Gviz: Given transcript names and TxDb, how do you plot grouped transcripts?

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