User: endrebak
endrebak • 760
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https://www.ntnu.edu/employees/endrebak
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Posts by endrebak
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... I know :) . I use it in my pyranges-library to write to bigwig: https://github.com/biocore-ntnu/pyranges ...
written 14 days ago by
endrebak • 760
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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 14 days ago by
endrebak • 760
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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 15 days ago by
endrebak • 760
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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 weeks ago by
endrebak • 760
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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 9 weeks ago by
endrebak • 760
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... I am partial to https://github.com/biocore-ntnu/pyranges ...
written 9 weeks ago by
endrebak • 760
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... epic2 supports this: https://github.com/biocore-ntnu/epic2
It also accepts bam, btw XD ...
written 9 weeks ago by
endrebak • 760
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... epic is currently deprecated in favor of epic2. epic2 does not support bigwig creation, but I might add a recipe on how to create the same bigwigs with pyranges. Would only be a few lines of code :) ...
written 9 weeks ago by
endrebak • 760
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Answer:
A: Create bigwigs in python?
... Using pyBigWig, I've created a higher-level API for this in PyRanges:
```
import pyranges as pr
chromsizes = pr.db.ucsc.chromosome_sizes("hg19") # getting data using mysql
gr = pr.data.chipseq() # get some test data
gr.out.bigwig("newpath/chipseq.bw", chromsizes)
```
More info at https://biocore-nt ...
written 9 weeks ago by
endrebak • 760
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... How do I merge the lists of reverse strand and forward strand genomicranges? ...
written 9 weeks ago by
endrebak • 760
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