Moderator: Alex Reynolds

gravatar for Alex Reynolds
Alex Reynolds30k
Reputation:
30,110
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Location:
Seattle, WA USA
Website:
http://bitsumma.com/
Twitter:
AlexReynolds
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Google Scholar Page
Last seen:
11 minutes ago
Joined:
10 years, 7 months ago
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a************@gmail.com

One of the developers behind the fast BEDOPS suite, whose pug Zac is the bestest pug in the world.

Posts by Alex Reynolds

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Answer: A: How can I remove the outliers from a boxplot and fill the groups?
... If you want clarity about and control over how you deal with outliers, without dealing with the "blackbox" that other people's code provides, there are a couple common approaches you can use to do this yourself: 1. Trimming 2. Winsorization In both approaches, you specify a percentage cutoff. You ...
written 2 days ago by Alex Reynolds30k
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Comment: C: Get the location of a promoter from a gene
... Could you use [CAGE TSS peaks][1], and then go upstream of the midpoint by some number of bases to define a proximal promoter (e.g., 1kb, 2kb, 5kb, etc.)? [1]: https://fantom.gsc.riken.jp/5/data/ ...
written 16 days ago by Alex Reynolds30k
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Comment: C: How do I calculate Jaccard distance between pair-wise OTUs species
... Euclidean and Jaccard distances are entirely different. ...
written 17 days ago by Alex Reynolds30k
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Comment: C: Identification and annotation of transposable elements in genomes
... https://link.springer.com/protocol/10.1007/978-1-4939-9074-0_6 ...
written 19 days ago by Alex Reynolds30k
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Comment: C: bootstraped spearman correlation in R
... The `spearmanRho` function uses [the `stats::cor` function][1] to calculate `rho`. Bootstrapping a certain number of times (the parameter `R` or 1000 times in your example) then gives you a confidence interval around that measurement of `rho`. [1]: https://www.rdocumentation.org/packages/stats/v ...
written 20 days ago by Alex Reynolds30k
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Answer: A: Merge several bigWig files (with different intervals) into single GRanges object
... You could do something efficiently via `bedmap` on the command-line: $ bedmap --echo --echo-map-score --delim '\t' <(bedops --partition A.bed B.bed) <(bedops --everything A.bed B.bed) > answer.bed Here, the reference set (from which intervals are derived) is the disjoint partition of ...
written 28 days ago by Alex Reynolds30k
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Answer: C: How to identify the bp distance of blast results to closest genes in a genome
... BEDOPS `gff2bed` and `closest-features` work with BLAST output via `-outfmt 6`. You could use the `--dist` option to report the distance between the hit and its nearest element. Ref. https://bedops.readthedocs.io/en/latest/content/reference/set-operations/closest-features.html ...
written 5 weeks ago by Alex Reynolds30k
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Comment: C: How to tell if a BigWig file is 1-based or 0-based?
... Not sure about the answer to your first question, but the second seems straightforward. Create a text file called `readBigWigHeader.py` and add the following code or similar: #!/usr/bin/env python import sys, pyBigWig fn = sys.argv[1] bw = pyBigWig.open(fn) sys.stdout.write("{}\ ...
written 6 weeks ago by Alex Reynolds30k
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Comment: C: How to tell if a BigWig file is 1-based or 0-based?
... Using Devon Ryan's Python library may help ( https://github.com/deeptools/pyBigWig ). Once installed: $ python >>> import pyBigWig >>> bw = pyBigWig.open("my.bigWig") >>> print(bw.header()) ...
written 6 weeks ago by Alex Reynolds30k
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Answer: A: Bedtools intersect with header file
... If you use bash, one option is to use tools that support Unix streams: $ bedops --intersect <(sort-bed A.txt) <(sort-bed B.txt) | cat <(head -1 A.txt) - > answer.bed Replace `head -1` with adjustments from `-1` to whatever number of header lines you have in `A.txt`. ...
written 7 weeks ago by Alex Reynolds30k

Latest awards to Alex Reynolds

Student 29 days ago, asked a question with at least 3 up-votes. For Tips On Compiling And Using Meme 4.3 With A Sun Grid Engine Computation Cluster
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Scholar 4 weeks ago, created an answer that has been accepted. For A: No PhyloP score for first stretch of chromosome?
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: Download Clustal Omega on Mac OS
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Great Question 9 weeks ago, created a question with more than 5,000 views. For Tips On Compiling And Using Meme 4.3 With A Sun Grid Engine Computation Cluster
Scholar 10 weeks ago, created an answer that has been accepted. For A: No PhyloP score for first stretch of chromosome?
Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: Download Clustal Omega on Mac OS
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Strategy For Dealing With Reference Files (Genomes) That Are Larger Than The Sof
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Appreciated 10 weeks ago, created a post with more than 5 votes. For Automating Gorilla And/Or Revigo Analysis
Appreciated 11 weeks ago, created a post with more than 5 votes. For Automating Gorilla And/Or Revigo Analysis
Scholar 12 weeks ago, created an answer that has been accepted. For A: No PhyloP score for first stretch of chromosome?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Scholar 3 months ago, created an answer that has been accepted. For A: No PhyloP score for first stretch of chromosome?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Scholar 3 months ago, created an answer that has been accepted. For A: No PhyloP score for first stretch of chromosome?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: How To Create Mutation Diagram In R Or In Any Tools?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?

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