User: endrebak
endrebak • 790
- Reputation:
- 790
- Status:
- Trusted
- Location:
- github.com/endrebak
- Website:
- https://github.com/end...
- Last seen:
- 2 days, 9 hours ago
- Joined:
- 3 years, 5 months ago
- Email:
- e*******@ntnu.no
https://www.ntnu.edu/employees/endrebak
https://github.com/endrebak
Posts by endrebak
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... I would love to try to help you. Can you post an issue on the repo? ...
written 25 days ago by
endrebak • 790
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... 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
endrebak • 790
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... Thanks! I did read the file format specification :) Strange it said nothing there. ...
written 10 weeks ago by
endrebak • 790
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... 426 rows in the GWAS catalogue contain x in the CHR_POS, like '31776605 x 95917441'
What does it mean? ...
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... I know :) . I use it in my pyranges-library to write to bigwig: https://github.com/biocore-ntnu/pyranges ...
written 3 months ago by
endrebak • 790
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... 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
endrebak • 790
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... 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. ...
written 3 months ago by
endrebak • 790
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1
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... 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
endrebak • 790
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... 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
endrebak • 790
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3
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... I am partial to https://github.com/biocore-ntnu/pyranges ...
written 5 months ago by
endrebak • 790
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
10 weeks ago,
created a question with more than 1,000 views.
For Fast datastructure to get counts of overlapping reads per nucleotide (!) in Python?
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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,
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For How do I filter a bam on length with pybedtools?
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14 months ago,
created a question with more than 1,000 views.
For Create bigwigs in python?
Centurion
15 months ago,
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Popular Question
23 months ago,
created a question with more than 1,000 views.
For Script to compute the effective genome size: epic-effective
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2.4 years ago,
created a question with more than 1,000 views.
For epic: new ChIP-Seq caller based on the SICER algorithm
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2.8 years ago,
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For A: How To Convert Gencode Gtf Into Bed Format ?
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3.0 years ago,
voted more than 100 times.
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3.1 years ago,
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For I want to store a docker image reproducing a paper. Is there a host for docker images of studies?
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3.1 years ago,
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For A: Given a link that displays genome browser data, how do I download a pdf using a
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3.1 years ago,
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For Fast datastructure to get counts of overlapping reads per nucleotide (!) in Python?
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