User: stianlagstad

gravatar for stianlagstad
stianlagstad90
Reputation:
90
Status:
Trusted
Location:
Last seen:
1 week, 6 days ago
Joined:
2 years ago
Email:
s***********@gmail.com

Posts by stianlagstad

<prev • 64 results • page 1 of 7 • next >
0
votes
2
answers
174
views
2
answers
Comment: C: Gviz: Help figuring out `arguments imply differing number of rows: 0, 1` error
... Thank you! :) ...
written 9 weeks ago by stianlagstad90
0
votes
2
answers
174
views
2
answers
Comment: C: Gviz: Help figuring out `arguments imply differing number of rows: 0, 1` error
... Thank you! :) ...
written 9 weeks ago by stianlagstad90
4
votes
2
answers
174
views
2
answers
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 11 weeks ago by stianlagstad90 • updated 10 weeks ago by Robert Ivanek460
0
votes
0
answers
92
views
0
answers
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 3 months ago by stianlagstad90
0
votes
2
answers
175
views
2
answers
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 7 months ago by stianlagstad90
0
votes
2
answers
175
views
2
answers
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 7 months ago by stianlagstad90
0
votes
0
answers
383
views
0
answers
Comment: C: Gviz/Biostrings memory issue?
... Alright. Thanks again! ...
written 14 months ago by stianlagstad90
0
votes
0
answers
383
views
0
answers
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 14 months ago by stianlagstad90
0
votes
0
answers
383
views
0
answers
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 14 months ago by stianlagstad90
0
votes
0
answers
383
views
0
answers
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 14 months ago by stianlagstad90

Latest awards to stianlagstad

Supporter 22 months ago, voted at least 25 times.
Scholar 22 months ago, created an answer that has been accepted. For A: Gviz: Given transcript names and TxDb, how do you plot grouped transcripts?
Scholar 23 months ago, created an answer that has been accepted. For A: Gviz: Given transcript names and TxDb, how do you plot grouped transcripts?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 163 users visited in the last hour