Questions tagged [pyranges]
The pyranges tag has no usage guidance.
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Compare in Python / PyRanges two genomic intervals to determine whether they're separate, partially overlapping, or contained
As part of a larger analysis, I need to evaluate pairs of genomic regions (regionsA and regionsB) and perform different ...
- 131
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1
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52
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Assign score to PyRanges from another PyRanges object
I have two PyRanges objects. PR1 is a set of regions of interest across a chromosome, PR2 tiles the genome and has a score associated with each range.
I need a way to get for each range in PR1 its ...
- 300
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How to adjust #columns shown when PyRange is printed?
In Pandas, we have pandas.options.display to adjust how a DataFrame should be displayed when printed.
I wonder if PyRanges has a ...
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How to add N bases to PyRange object (i.e., shifting PyRanges coordinates)
I would like to add n (e.g., 1k) bases to a PyRange object (i.e., shifting PyRanges coordinates).
How can I do that?
Input:
...
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848
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235
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Create new range based from existing range (python)
I have a pyranges object that I am looking to iterate over. For each range, I would like to "resize" it to its centre (so start+end/2) and save that into ...
- 300
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532
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Efficiently iterate over bed and subset pyranges objects
I am using pyranges and I have two datasets that I want to compare in several genome-wide intervals based on a bed file.
For every interval in the bed file, I want to get all overlapping positions ...
- 1,314
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Summing two columns where they share interval overlap
I have two bed files where each column has a numeric score. I want to sum these numbers where there is overlap between the two bed files. How do I do that? Also, I am only interested in the score in ...
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