User: steve

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steve1.1k
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Posts by steve

<prev • 114 results • page 1 of 12 • next >
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Comment: C: Organizing a Bioinformatics Conference ?
... I've found parallel sessions most effective when topics are divided into categories such as "Beginner - Intermediate - Advanced", so they might have more mutually exclusive audiences. ...
written 3 days ago by steve1.1k
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Answer: A: Wait For A Job To Complete And Give Results Before Starting A New One
... Old question, but for anyone who likes Python and is trying to manage HPC cluster job submissions, I came up with a module for this [here](https://github.com/NYU-Molecular-Pathology/util/blob/master/qsub.py). You can run the module directly as a script (`python qsub.py`) for a demo. Usage: $ ...
written 3 days ago by steve1.1k
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Comment: C: Genome Informatics meeting software list
... when was the meeting? I think I missed it :( ...
written 12 days ago by steve1.1k
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Converting variant identifiers to genomic coordinates
... How do you find the .bed formatted genomic coordinates (chrom - start - stop, or even just chrom - pos) for variants if you are given information such as "NT5C2 c.1224C>A" or "KRAS p.G12D" ? It looks like the answers [here](https://www.biostars.org/p/107493/) are close, but they appear to req ...
variant written 13 days ago by steve1.1k
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Answer: A: For loop script
... There are numerous issues with your script, you might want to spend some time checking out some of [these tutorials](https://www.google.com/search?q=bash+script+tutorial&ie=utf-8&oe=utf-8) brush some more syntax and formatting that will fix some of the problems. I reformatted it to look a ...
written 16 days ago by steve1.1k
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Comment: C: Retrieve data from Excel sheet for Mysql table
... going to need to see an actual sample of the data to be able to make a suggestion ...
written 16 days ago by steve1.1k
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Comment: C: For loop script
... Its a little hard to read your script since it is not formatted properly in the post, but something that immediately jumps out is that you are calling `sh` shell, but you are using `[[ ... ]]` for test, which I believe are `bash` specific and not supported in `sh`. Is there a reason you are running ...
written 16 days ago by steve1.1k
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Comment: C: Retrieve data from Excel sheet for Mysql table
... Also it sounds like you have your data in a wide format, I think for a SQL database you might want it in long format instead. I typically use R for processing tabular data, particularly with the `reshape2::melt` function to convert from wide to long; details [here](http://seananderson.ca/2013/10/19/ ...
written 16 days ago by steve1.1k
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Comment: C: Retrieve data from Excel sheet for Mysql table
... I would suggest just dumping the data to a tabular format such as .tsv or .csv and then importing it into the DB that way. I've got a quick & easy Python script to dump .xlsx using Pandas [here](https://github.com/stevekm/toolbox/blob/a316c85117ae57f7bdf72bdfc9414da3d261bc82/dump_xlsx.py) ...
written 16 days ago by steve1.1k
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Comment: C: Sanger sequencing is no longer the gold standard?
... would love to see the code for your pipeline, if available ...
written 17 days ago by steve1.1k

Latest awards to steve

Teacher 16 days ago, created an answer with at least 3 up-votes. For A: Visualization of Homer mergePeaks output Venn?
Guru 16 days ago, received more than 100 upvotes.
Appreciated 22 days ago, created a post with more than 5 votes. For Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
Centurion 22 days ago, created 100 posts.
Great Question 11 weeks ago, created a question with more than 5,000 views. For Creating Interactive Volcano Plots with R and Plot.ly
Appreciated 3 months ago, created a post with more than 5 votes. For Automatic IGV snapshot script
Popular Question 4 months ago, created a question with more than 1,000 views. For How to tell which transcript is the canonical transcript?
Popular Question 5 months ago, created a question with more than 1,000 views. For Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
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Appreciated 7 months ago, created a post with more than 5 votes. For Automatic IGV snapshot script
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Student 8 months ago, asked a question with at least 3 up-votes. For How to tell which transcript is the canonical transcript?
Popular Question 11 months ago, created a question with more than 1,000 views. For Creating Interactive Volcano Plots with R and Plot.ly
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Appreciated 13 months ago, created a post with more than 5 votes. For Creating Interactive Volcano Plots with R and Plot.ly
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Scholar 18 months ago, created an answer that has been accepted. For A: Visualization of Homer mergePeaks output Venn?
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