Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In

User: endrebak

gravatar for endrebak
endrebak • 640
Reputation:
640
Status:
Trusted
Location:
Website:
https://github.com/end...
Last seen:
2 weeks, 4 days ago
Joined:
2 years, 3 months ago
Email:
e*******@ntnu.no

https://www.ntnu.edu/employees/endrebak

https://github.com/endrebak

 

Posts by endrebak

<prev • 102 results • page 1 of 11 • next >
0
votes
0
answers
120
views
0
answers
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 28 days ago by endrebak • 640
0
votes
0
answers
120
views
0
answers
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 4 weeks ago by endrebak • 640 • updated 28 days ago by bruce.moran • 410
0
votes
15
answers
27k
views
15
answers
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 8 weeks ago by endrebak • 640
1
vote
2
answers
2.2k
views
2
answers
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 8 weeks ago by endrebak • 640
1
vote
0
answers
165
views
0
answers
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 8 weeks ago by endrebak • 640
2
votes
0
answers
165
views
0
answers
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 8 weeks ago by endrebak • 640
0
votes
2
answers
188
views
2
answers
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 10 weeks ago by endrebak • 640
0
votes
2
answers
188
views
2
answers
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 10 weeks ago by endrebak • 640
0
votes
2
answers
188
views
2
answers
Comment: C: Algorithms for finding nearest range given two lists of ranges?
... Agreed. Sorry about that. ...
written 10 weeks ago by endrebak • 640
0
votes
15
answers
27k
views
15
answers
Comment: C: What Is The Quickest Algorithm For Range Overlap?
... https://github.com/hunt-genes/ncls ...
written 10 weeks ago by endrebak • 640

Latest awards to endrebak

Centurion 4 weeks ago, created 100 posts.
Popular Question 9 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 epic: new ChIP-Seq caller based on the SICER algorithm
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: How To Convert Gencode Gtf Into Bed Format ?
Voter 22 months ago, voted more than 100 times.
Student 23 months 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 23 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
Student 23 months ago, asked a question with at least 3 up-votes. For Fast datastructure to get counts of overlapping reads per nucleotide (!) in Python?
Supporter 2.2 years ago, voted at least 25 times.
Appreciated 2.3 years ago, created a post with more than 5 votes. For epic: new ChIP-Seq caller based on the SICER algorithm
Autobiographer 2.3 years ago, has more than 80 characters in the information field of the user's profile.
Appreciated 2.3 years ago, created a post with more than 5 votes. For epic: new ChIP-Seq caller based on the SICER algorithm
Student 2.3 years ago, asked a question with at least 3 up-votes. For epic: new ChIP-Seq caller based on the SICER algorithm
Commentator 2.3 years ago, created a comment with at least 3 up-votes. For C: SICER raw data
Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1454 users visited in the last hour