Moderator: Ryan Dale

gravatar for Ryan Dale
Ryan Dale4.6k
Reputation:
4,570
Status:
Trusted
Location:
Bethesda, MD
Website:
https://github.com/daler
Twitter:
@daler_t
Scholar ID:
Google Scholar Page
Last seen:
2 days, 21 hours ago
Joined:
7 years, 3 months ago
Email:
d*****@niddk.nih.gov

A benthic ecologist by training, but now a bioinformatician at NIH's National Institute of Diabetes and Digestive and Kidney Diseases, Laboratory of Cellular and Developmental Biology.

Currently studying the relationship of chromatin conformation and gene regulation.

Please note: any opinions expressed here are my own and not those of my employer.

Posts by Ryan Dale

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Comment: C: ChromHMM Output Descriptions
... The label of each state is subjective. Coming up with good labels requires looking carefully at the enrichments (from running OverlapEnrichment) and emissions heatmaps to decide what you want to name them. ...
written 9 weeks ago by Ryan Dale4.6k
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Comment: C: Output bed file region sizes as histogram
... Sounds like you're running on a headless server with no X11 windows. In that case add these two lines to the very beginning: import matplotilb matplotlib.use('agg') see http://stackoverflow.com/questions/2801882/generating-a-png-with-matplotlib-when-display-is-undefined for more details an ...
written 6 months ago by Ryan Dale4.6k
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Answer: A: Output bed file region sizes as histogram
... If you have enough RAM and are OK with Python: import pybedtools from matplotlib import pyplot as plt sizes = [len(i) for i in pybedtools.BedTool('my.bed')] plt.hist(sizes) plt.savefig('hist.png') plt.show() ...
written 6 months ago by Ryan Dale4.6k
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Answer: A: How to fix my broken GTF file?
... The `gffutils` python package can help with this: https://daler.github.io/gffutils It will infer the gene and transcript extents; doing so is the default behavior for GTF files. The following will import the GTF into a sqlite3 database (which you can use for other things if needed) and then output ...
written 6 months ago by Ryan Dale4.6k
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Comment: C: How to apply ChromHMM on ChromImpute output?
... As you mention, ChromHMM expects read counts. Even if you transform your data somehow to make it work with ChromHMM, how will you interpret the results? I would expect the HMM to see the imputed data as a combination of the other vars anyway, making it redundant. I guess I'm not sure there's an adva ...
written 6 months ago by Ryan Dale4.6k
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Comment: C: csvtk - a cross-platform, efficient, practical and pretty CSV/TSV toolkit
... FYI, versions 0.4.4 thru 0.7.0 are available for Linux & OSX via [bioconda][1] [1]: https://bioconda.github.io ...
written 8 months ago by Ryan Dale4.6k
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Job: Bioinformatics trainee position at NIH (Bethesda, MD, USA)
... We have an opening for a post-baccalaureate bioinformatics trainee in the Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases at the National Institutes of Health in Bethesda, MD. This is a one year appointment, starting as soon as May 2 ...
job written 9 months ago by Ryan Dale4.6k • updated 9 months ago by Sinji2.5k
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Answer: A: ChIP-seq vs. RNA-seq
... Map them both to a reference; the RNA-seq library will be more likely to have splice junctions (look for "N" in the BAM cigar string) and will be sparse in intergenic regions, while the ChIP-seq will have more even coverage, less dynamic range, and will probably have some low-level signal in most pl ...
written 10 months ago by Ryan Dale4.6k
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Comment: C: Do specialized Hi-C databases exist?
... Fidel, this is amazing. A much-needed and much-appreciated initiative. ...
written 10 months ago by Ryan Dale4.6k
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Comment: C: ChIPseq - Identical peaks in IP and input samples
... Are you using a Clontech kit by any chance? ...
written 12 months ago by Ryan Dale4.6k

Latest awards to Ryan Dale

Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Visualizing Genomic Interactions
Scholar 6 months ago, created an answer that has been accepted. For A: Making gene annotation from a GTF file
Scholar 6 months ago, created an answer that has been accepted. For A: Creatig TrackHubs from BigWigs
Popular Question 7 months ago, created a question with more than 1,000 views. For Bioinformatics trainee position at NIH
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Visualizing Genomic Interactions
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Visualizing Genomic Interactions
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Visualizing Genomic Interactions
Scholar 14 months ago, created an answer that has been accepted. For A: Making gene annotation from a GTF file
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Visualizing Genomic Interactions
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Visualizing Genomic Interactions
Scholar 15 months ago, created an answer that has been accepted. For A: Making gene annotation from a GTF file
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Visualizing Genomic Interactions
Scholar 15 months ago, created an answer that has been accepted. For A: Making gene annotation from a GTF file
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Samtools View - What'S The Purpose Of The -T Option?
Good Answer 16 months ago, created an answer that was upvoted at least 5 times. For A: Samtools View - What'S The Purpose Of The -T Option?
Scholar 16 months ago, created an answer that has been accepted. For A: Making gene annotation from a GTF file
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Visualizing Genomic Interactions
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Visualizing Genomic Interactions
Scholar 17 months ago, created an answer that has been accepted. For A: Making gene annotation from a GTF file
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Visualizing Genomic Interactions
Good Answer 17 months ago, created an answer that was upvoted at least 5 times. For A: Samtools View - What'S The Purpose Of The -T Option?
Scholar 18 months ago, created an answer that has been accepted. For A: Making gene annotation from a GTF file

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