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User: endrebak

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endrebak • 680
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680
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2 months, 2 weeks ago
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2 years, 5 months ago
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Posts by endrebak

<prev • 102 results • page 1 of 11 • next >
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Comment: C: Can genomicranges do bedtools-like intersection operations?
... Okay, thanks. I am not that interested in the actual way of doing it, I was just wondering if it was possible without hand rolling a solution. It seems like most genomicranges operations are set-like. ...
written 12 weeks ago by endrebak • 680
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Can genomicranges do bedtools-like intersection operations?
... In bedtools intersect means "for each read in A, for each read in B that overlaps, find the part of A that overlaps with a read in B". So that if you have 4 reads in A and 6 reads in B and all overlap you get 4*6 results. GenomicRanges intersect works differently; for both A and B it first cluste ...
R written 3 months ago by endrebak • 680 • updated 12 weeks ago by bruce.moran • 410
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Answer: A: What Is The Quickest Algorithm For Range Overlap?
... The fastest implementation in Python I have found in is the Nested Containment List. It is several times faster than the ultrafast intervaltrees found in the kernel. pygr has died from bitrot, but I have revived the underlying datastructure here: https://github.com/hunt-genes/ncls This datastructur ...
written 4 months ago by endrebak • 680
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Answer: A: Handling Ranged Data In Python
... You now can: https://github.com/endrebak/pyranges It is still in pre-alpha, but will be updated by me as I use it all the time. ...
written 4 months ago by endrebak • 680
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Comment: C: (pre-alpha) pyranges: performant, pythonic GenomicRanges
... BioRanges was never finished and I have seen no timings. PyRanges seems to be reaching feature parity with GenomicRanges soon. The greatest difference is perhaps that I try to make a dinky convenient wrapper around pandas dfs so that all the good stuff from GenomicRanges can be used on dfs while sti ...
written 4 months ago by endrebak • 680
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Tool: (pre-alpha) pyranges: performant, pythonic GenomicRanges
... GenomicRanges for Python. This library tries to be a thin, but extremely useful wrapper around genomic data contained in pandas dataframes. This allows for all the wonderful functionality of bedtools/bedops and/or GenomicRanges, while being able to use the the enormous universe of Python datascienc ...
python genomicranges tool written 4 months ago by endrebak • 680
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Comment: C: Algorithms for finding nearest range given two lists of ranges?
... https://github.com/bedops/bedops/blob/master/applications/bed/closestfeats/src/ClosestFeature.cpp Thanks. Iff sorting is much faster than KD-tree construction, I'll try to use your method (I suspect it'll be the other way around though). ...
written 4 months ago by endrebak • 680
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Comment: C: Algorithms for finding nearest range given two lists of ranges?
... Brilliant. There is both a scipy implementation: https://docs.scipy.org/doc/scipy-0.15.1/reference/generated/scipy.spatial.KDTree.html#scipy.spatial.KDTree and a C library that seems like it'll be easy to wrap: https://github.com/jtsiomb/kdtree ...
written 4 months ago by endrebak • 680
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Comment: C: Algorithms for finding nearest range given two lists of ranges?
... Agreed. Sorry about that. ...
written 4 months ago by endrebak • 680
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Comment: C: What Is The Quickest Algorithm For Range Overlap?
... https://github.com/hunt-genes/ncls ...
written 4 months ago by endrebak • 680

Latest awards to endrebak

Centurion 3 months ago, created 100 posts.
Popular Question 11 months ago, created a question with more than 1,000 views. For Script to compute the effective genome size: epic-effective
Popular Question 16 months ago, created a question with more than 1,000 views. For epic: new ChIP-Seq caller based on the SICER algorithm
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: How To Convert Gencode Gtf Into Bed Format ?
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Student 2.1 years ago, asked a question with at least 3 up-votes. For I want to store a docker image reproducing a paper. Is there a host for docker images of studies?
Scholar 2.1 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 2.1 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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Appreciated 2.5 years ago, created a post with more than 5 votes. For epic: new ChIP-Seq caller based on the SICER algorithm
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