User: stianlagstad

gravatar for stianlagstad
stianlagstad880
Reputation:
880
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Trusted
Location:
Oslo, Norway
Website:
http://stianlagstad.no/
Twitter:
stianlagstad
Last seen:
8 hours ago
Joined:
2 years, 7 months ago
Email:
s***********@gmail.com

Posts by stianlagstad

<prev • 23 results • page 1 of 3 • next >
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Comment: C: Extract rows if 2 column values has 21 in between
... What do you mean by "21 in between"? Since you list the interval "6 15" in your desired output I don't understand it. ...
written 19 months ago by stianlagstad880
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Comment: C: Plot reads from .BAM file above reference sequence in R?
... Thank you, but rest assured that I've done more than a few searches and I've looked at more than a couple of packages before coming here to ask the question. If you have a specific suggestion that would be helpful :) ...
written 19 months ago by stianlagstad880
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Comment: C: R data frame - last line plotted with line 1
... Here is your image, since you didn't have the correct url in your post: ![enter image description here][1] I don't know how to solve your problem, but if you haven't figured it out in a few days you could post a question on [the Bioconductor support site][2]. [The Sushi author][3] seems to be acti ...
written 19 months ago by stianlagstad880
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Comment: C: Plot reads from .BAM file above reference sequence in R?
... Thank you for the answer! I have looked at the Sushi manual before but I couldn't see anything that would help me. Could you point me in the right direction? ...
written 19 months ago by stianlagstad880
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Comment: C: Plot reads from .BAM file above reference sequence in R?
... Thank you for the answer! For a single case it would be easier to do it manually, but I have to do this automatically in R :) I have a solution that works with Gviz, but that empty space is giving me problems when I export the plot in scalable formats. ...
written 19 months ago by stianlagstad880
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Comment: C: R data frame - last line plotted with line 1
... You can upload the plot [here][1], and include it in your post like this: ![enter image description here][2] It would also be helpful if you included example code that leads to the problem you're having. [1]: http://postimage.org/ [2]: http://s31.postimg.org/9l3odospn/paint.jpg ...
written 19 months ago by stianlagstad880
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Answer: A: How to build Biostar?
... [Biostar on GitHub][1]. Install instructions [here][2]. [Question2Answer on GitHub][3]. Install instructions [here][4]. Here is a question on stackoverflow you might want to look at: [Stack Exchange clones][5]. You might find something that's in a language you're familiar with there. [1]: http ...
written 19 months ago by stianlagstad880
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Plot reads from .BAM file above reference sequence in R?
... I want to plot something like this: ![enter image description here][1] This was produced with Gviz. My problem with Gviz is the empty space added at the bottom of the plot (below the reads). I posted a question about that [here][2]. Do you have any suggestions on how I can plot reads aligned to a ...
R plot written 19 months ago by stianlagstad880
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Comment: C: R&Bioconductor: Extract coverage from bamfile given GRanges object?
... For my real script I do that in an earlier step, but thanks! ...
written 19 months ago by stianlagstad880
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Answer: A: R&Bioconductor: Extract coverage from bamfile given GRanges object?
... I think I figured it out: library(Rsamtools) library(RNAseqData.HNRNPC.bam.chr14) library(TxDb.Hsapiens.UCSC.hg19.knownGene) # Get reference to example bamfile bamfile <- RNAseqData.HNRNPC.bam.chr14_BAMFILES[1] # Exmple transcript name transcript <- "uc001yhh ...
written 19 months ago by stianlagstad880

Latest awards to stianlagstad

Popular Question 11 weeks ago, created a question with more than 1,000 views. For Gviz: How to plot transcripts with grouping given transcript names and a TxDb?
Scholar 19 months ago, created an answer that has been accepted. For A: Gviz: How to plot transcripts with grouping given transcript names and a TxDb?
Popular Question 23 months ago, created a question with more than 1,000 views. For Which program, tool, or strategy do you use to visualize genomic rearrangements?
Librarian 23 months ago, created a post with more than 10 bookmarks. For Which program, tool, or strategy do you use to visualize genomic rearrangements?
Prophet 2.2 years ago, created a post with more than 20 followers. For Which program, tool, or strategy do you use to visualize genomic rearrangements?
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: Gene Fusion Detection: Rna-Seq Data
Good Question 2.2 years ago, asked a question that was upvoted at least 5 times. For Which program, tool, or strategy do you use to visualize genomic rearrangements?
Student 2.2 years ago, asked a question with at least 3 up-votes. For Which program, tool, or strategy do you use to visualize genomic rearrangements?
Good Answer 2.2 years ago, created an answer that was upvoted at least 5 times. For A: Gene Fusion Detection: Rna-Seq Data
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: Gene Fusion Detection: Rna-Seq Data
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Gene Fusion Detection: Rna-Seq Data

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