User: steve

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steve1.3k
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Posts by steve

<prev • 136 results • page 1 of 14 • next >
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Answer: A: Can I install and run igvtools on a server?
... You can run IGV from a remote server, provided that you have X11 installed on the remote server ([https://en.wikipedia.org/wiki/X_Window_System][1]) and an X11 window program on the local machine. On a Mac, you would: - make sure you have [XQuartz][2] installed - `ssh` into your server with the ...
written 16 hours ago by steve1.3k
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Comment: C: Help to install a computer to analyze the data
... there are some links in the comments here: https://www.biostars.org/p/154251/ ...
written 16 hours ago by steve1.3k
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Comment: C: How To Convert Gencode Gtf Into Bed Format ?
... its worth noting that the Makefile there was developed based on the answers here ...
written 11 days ago by steve1.3k
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Comment: C: Workflow management software for pipeline development in NGS
... Not so much a 'problem', but a lot of Bioinformatics is done in R or Python or even just shell scripting, so coming from that background Groovy seems very alien. I've spent a lot of time the past weeks trying to figure out how Nextflow works and the combination of Groovy + Domain Specific Language h ...
written 14 days ago by steve1.3k
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Comment: C: Using DRMAA in bioinformatics workflows?
... I actually did write my own wrapper library for SGE [here](https://github.com/NYU-Molecular-Pathology/util/blob/master/qsub.py), but the task is non-trivial, and we'll soon be moving to SLURM as well, which would need yet another wrapper, plus another module to abstract out the SGE/SLURM specific pa ...
written 14 days ago by steve1.3k
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Comment: C: Looking for any entry level Bioinformatics job
... look at university websites for job listings, and look for university labs that may be hiring ...
written 15 days ago by steve1.3k
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Comment: C: Counting number of bases covered across multiple bam files
... would you happen to have a small code sample that shows how to do this? ...
written 20 days ago by steve1.3k
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Answer: A: How to Visulaise Genes per sample (Text visualisation)
... If I am allowed to post two answers, I just figured this one out and like it better #!/usr/bin/env Rscript # visualize a character matrix # install.packages("DiagrammeR") library("DiagrammeR") data <- structure(list(gene = structure(c(8L, 18L, 10L, 3L, 4L, ...
written 26 days ago by steve1.3k
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Answer: A: How to Visulaise Genes per sample (Text visualisation)
... Here is something that does what you request, in R #!/usr/bin/env Rscript # visualize a character matrix library("ggplot2") # install.packages("ggrepel") library("ggrepel") # for spreading text labels on the plot lines <- " MED20_Average Glycyrrhizic_ ...
written 26 days ago by steve1.3k
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Comment: C: how to draw two different Y-axes with deeptools?
... I have a workflow where I did this [here](https://github.com/stevekm/Bioinformatics/blob/56f966ac7268fcacb141b4af7e4a02a2c4207d18/misc_workflow/genomic_region_profiles.Rmd). It was a bit of an iterative trial&error process, but there might be some useful code scraps mixed in there. ...
written 6 weeks ago by steve1.3k

Latest awards to steve

Popular Question 19 days ago, created a question with more than 1,000 views. For How to tell which transcript is the canonical transcript?
Popular Question 6 weeks ago, created a question with more than 1,000 views. For How to tell which transcript is the canonical transcript?
Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: StackExchange/Area51 bioinformatics is back
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Visualization of Homer mergePeaks output Venn?
Guru 11 weeks ago, received more than 100 upvotes.
Appreciated 12 weeks ago, created a post with more than 5 votes. For Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
Centurion 12 weeks ago, created 100 posts.
Great Question 4 months ago, created a question with more than 5,000 views. For Creating Interactive Volcano Plots with R and Plot.ly
Appreciated 5 months ago, created a post with more than 5 votes. For Automatic IGV snapshot script
Popular Question 6 months ago, created a question with more than 1,000 views. For How to tell which transcript is the canonical transcript?
Popular Question 7 months ago, created a question with more than 1,000 views. For Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: StackExchange/Area51 bioinformatics is back
Appreciated 9 months ago, created a post with more than 5 votes. For Automatic IGV snapshot script
Appreciated 10 months ago, created a post with more than 5 votes. For Automatic IGV snapshot script
Student 10 months ago, asked a question with at least 3 up-votes. For How to tell which transcript is the canonical transcript?
Popular Question 13 months ago, created a question with more than 1,000 views. For Creating Interactive Volcano Plots with R and Plot.ly
Voter 13 months ago, voted more than 100 times.
Appreciated 16 months ago, created a post with more than 5 votes. For Creating Interactive Volcano Plots with R and Plot.ly
Student 17 months ago, asked a question with at least 3 up-votes. For How to tell which transcript is the canonical transcript?
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Scholar 20 months ago, created an answer that has been accepted. For A: Visualization of Homer mergePeaks output Venn?
Scholar 21 months ago, created an answer that has been accepted. For A: Visualization of Homer mergePeaks output Venn?
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Visualization of Homer mergePeaks output Venn?

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