User: endrebak

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endrebak760
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https://github.com/endrebak
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2 weeks ago
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3 years, 2 months ago
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Posts by endrebak

<prev • 125 results • page 1 of 13 • next >
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Comment: C: Loading bigiwg into an an array in javascript?
... I know :) . I use it in my pyranges-library to write to bigwig: https://github.com/biocore-ntnu/pyranges ...
written 14 days ago by endrebak760
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Comment: C: Loading bigiwg into an an array in javascript?
... 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 endrebak760
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Loading bigiwg into an an array in javascript?
... 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. ...
bigwig javascript written 15 days ago by endrebak760
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Comment: C: New ultraperformant version of SICER/epic: epic2
... 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 endrebak760
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Answer: A: pythonic equivalent to reduce() in R GRanges - how to collapse ranged data?
... 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 endrebak760
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Answer: A: What Is The Best Library For Handling Interval Logic?
... I am partial to https://github.com/biocore-ntnu/pyranges ...
written 9 weeks ago by endrebak760
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Answer: A: Can EPIC call peaks on files without control?
... epic2 supports this: https://github.com/biocore-ntnu/epic2 It also accepts bam, btw XD ...
written 9 weeks ago by endrebak760
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Answer: A: Current status of EPIC peak caller
... 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 endrebak760
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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 endrebak760
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Comment: C: How do I split a genomicrange on chromosome and strand?
... How do I merge the lists of reverse strand and forward strand genomicranges? ...
written 9 weeks ago by endrebak760

Latest awards to endrebak

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?
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: How To Convert Gencode Gtf Into Bed Format ?
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Public paired end chip seq dataset, both ChIP and input?
Appreciated 11 months ago, created a post with more than 5 votes. For Script to compute the effective genome size: epic-effective
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: How To Convert Gencode Gtf Into Bed Format ?
Popular Question 11 months ago, created a question with more than 1,000 views. For Public paired end chip seq dataset, both ChIP and input?
Popular Question 11 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 11 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 11 months ago, created a question with more than 1,000 views. For Script to compute the effective genome size: epic-effective
Popular Question 11 months ago, created a question with more than 1,000 views. For How do I filter a bam on length with pybedtools?
Popular Question 11 months ago, created a question with more than 1,000 views. For Create bigwigs in python?
Centurion 12 months ago, created 100 posts.
Popular Question 20 months ago, created a question with more than 1,000 views. For Script to compute the effective genome size: epic-effective
Popular Question 2.1 years ago, created a question with more than 1,000 views. For epic: new ChIP-Seq caller based on the SICER algorithm
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: How To Convert Gencode Gtf Into Bed Format ?
Voter 2.8 years ago, voted more than 100 times.
Scholar 2.8 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 2.9 years ago, asked a question with at least 3 up-votes. For Fast datastructure to get counts of overlapping reads per nucleotide (!) in Python?
Supporter 3.1 years ago, voted at least 25 times.
Appreciated 3.2 years ago, created a post with more than 5 votes. For epic: new ChIP-Seq caller based on the SICER algorithm
Autobiographer 3.2 years ago, has more than 80 characters in the information field of the user's profile.
Appreciated 3.2 years ago, created a post with more than 5 votes. For epic: new ChIP-Seq caller based on the SICER algorithm
Student 3.2 years ago, asked a question with at least 3 up-votes. For epic: new ChIP-Seq caller based on the SICER algorithm

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