User: endrebak

gravatar for endrebak
endrebak790
Reputation:
790
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Trusted
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github.com/endrebak
Website:
https://github.com/end...
Last seen:
2 days, 9 hours ago
Joined:
3 years, 5 months ago
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e*******@ntnu.no

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Posts by endrebak

<prev • 129 results • page 1 of 13 • next >
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Comment: C: New ultraperformant version of SICER/epic: epic2
... I would love to try to help you. Can you post an issue on the repo? ...
written 25 days ago by endrebak790
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Answer: A: Fast datastructure to get counts of overlapping reads per nucleotide (!) in Pyth
... https://github.com/pyranges/pyrle Rle arithmetic for Python. Docs here: https://biocore-ntnu.github.io/pyranges/turning-ranges-into-rles.html and here https://biocore-ntnu.github.io/pyranges/an-introduction-to-rles.html ...
written 9 weeks ago by endrebak790
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Comment: C: What do the positions '31776605 x 95917441' mean in GWAS catalogue data?
... Thanks! I did read the file format specification :) Strange it said nothing there. ...
written 10 weeks ago by endrebak790
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What do the positions '31776605 x 95917441' mean in GWAS catalogue data?
... 426 rows in the GWAS catalogue contain x in the CHR_POS, like '31776605 x 95917441' What does it mean? ...
gwas-catalogue written 10 weeks ago by endrebak790 • updated 10 weeks ago by Corentin380
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Comment: C: Loading bigiwg into an an array in javascript?
... I know :) . I use it in my pyranges-library to write to bigwig: https://github.com/biocore-ntnu/pyranges ...
written 3 months ago by endrebak790
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Comment: C: Loading bigiwg into an an array in javascript?
... I know there are genome browsers that read bw (igv.js and others), so if I could use their functionality, it would be swell. In a standalone application. I was thinking someone knew how to use bigwig.js or something to load it. ...
written 3 months ago by endrebak790
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Loading bigiwg into an an array in javascript?
... I want to load a bigwig-file into an array in javascript. How do I do that? There are several libraries with bigwig-readers, but I am a newb. Plus points if you can show me how to only fetch data for a specific range. ...
bigwig javascript written 3 months ago by endrebak790
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Comment: C: New ultraperformant version of SICER/epic: epic2
... Macs2 is better for sharp peaks :) I've used epic2 for medium marks like PolII and H3K4me3, but not TFs with very sharp peaks. ...
written 4 months ago by endrebak790
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Answer: A: pythonic equivalent to reduce() in R GRanges - how to collapse ranged data?
... https://github.com/biocore-ntnu/pyranges import pyranges as pr chromosomes = [1] * 3 + [2] * 2 starts = [100, 200, 300, 100, 400] ends = [150, 350, 400, 500, 450] gr = pr.PyRanges(chromosomes=chromosomes, starts=starts, ends=ends) print(gr.cluster()) # +--------------+-- ...
written 5 months ago by endrebak790
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Answer: A: What Is The Best Library For Handling Interval Logic?
... I am partial to https://github.com/biocore-ntnu/pyranges ...
written 5 months ago by endrebak790

Latest awards to endrebak

Popular Question 9 days ago, created a question with more than 1,000 views. For Public paired end chip seq dataset, both ChIP and input?
Popular Question 25 days ago, created a question with more than 1,000 views. For Public paired end chip seq dataset, both ChIP and input?
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Public paired end chip seq dataset, both ChIP and input?
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Public paired end chip seq dataset, both ChIP and input?
Popular Question 3 months ago, created a question with more than 1,000 views. For Public paired end chip seq dataset, both ChIP and input?
Scholar 4 months ago, created an answer that has been accepted. For A: Given a link that displays genome browser data, how do I download a pdf using a
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How To Convert Gencode Gtf Into Bed Format ?
Popular Question 4 months ago, created a question with more than 1,000 views. For Public paired end chip seq dataset, both ChIP and input?
Appreciated 14 months ago, created a post with more than 5 votes. For Script to compute the effective genome size: epic-effective
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: How To Convert Gencode Gtf Into Bed Format ?
Popular Question 14 months ago, created a question with more than 1,000 views. For Public paired end chip seq dataset, both ChIP and input?
Popular Question 14 months ago, created a question with more than 1,000 views. For How do I make a bigwig file from a matrix of counts?
Popular Question 14 months ago, created a question with more than 1,000 views. For Different mappability/effective genome fraction with paired end reads? (ChIP-Seq)
Popular Question 14 months ago, created a question with more than 1,000 views. For Script to compute the effective genome size: epic-effective
Popular Question 14 months ago, created a question with more than 1,000 views. For How do I filter a bam on length with pybedtools?
Popular Question 14 months ago, created a question with more than 1,000 views. For Create bigwigs in python?
Centurion 15 months ago, created 100 posts.
Popular Question 23 months ago, created a question with more than 1,000 views. For Script to compute the effective genome size: epic-effective
Popular Question 2.4 years ago, created a question with more than 1,000 views. For epic: new ChIP-Seq caller based on the SICER algorithm
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: How To Convert Gencode Gtf Into Bed Format ?
Voter 3.0 years ago, voted more than 100 times.
Scholar 3.1 years ago, created an answer that has been accepted. For A: Given a link that displays genome browser data, how do I download a pdf using a
Student 3.1 years ago, asked a question with at least 3 up-votes. For Fast datastructure to get counts of overlapping reads per nucleotide (!) in Python?

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