User: endrebak

gravatar for endrebak
endrebak800
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800
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Trusted
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github.com/endrebak
Website:
https://github.com/end...
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2 weeks, 3 days ago
Joined:
3 years, 10 months ago
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Posts by endrebak

<prev • 134 results • page 1 of 14 • next >
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Answer: A: How do I compute ld blocks from the hapmap ld_data?
... Method: https://academic.oup.com/bioinformatics/article/32/2/283/1743626 Data: https://bitbucket.org/nygcresearch/ldetect-data/src/master/EUR/fourier_ls-all.bed ...
written 7 weeks ago by endrebak800
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Comment: C: How do I compute ld blocks from the hapmap ld_data?
... Ah, I had no idea. That makes sense :) ...
written 7 weeks ago by endrebak800
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Comment: C: How do I compute ld blocks from the hapmap ld_data?
... I thank you for your reply. I should have been more explicit; I wanted bed files with the ld-blocks to use in my analyses. ...
written 7 weeks ago by endrebak800
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How do I compute ld blocks from the hapmap ld_data?
... When people ask for ld blocks on this forum, this link is often posted: ftp://ftp.ncbi.nlm.nih.gov/hapmap/ld_data/latest However, those files merely contain the correlations between snps. How do I use these to compute ld-blocks? Would be nice if you could post an example script or invocation of a ...
snps ld written 7 weeks ago by endrebak800
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Global HMM annotation state bed for epigenome roadmap data?
... I can find lots of files that have the annotation state (TSS, Bivalent etc) for each cell type in the epigenome roadmap data, but is there a global file that shows the most common annotation state over all the cell types? Thanks. ...
roadmap epigenomics written 3 months ago by endrebak800
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Comment: C: New ultraperformant version of SICER/epic: epic2
... I would love to try to help you. Can you post an issue on the repo? ...
written 5 months ago by endrebak800
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Answer: A: Fast datastructure to get counts of overlapping reads per nucleotide (!) in Pyth
... https://github.com/pyranges/pyrle Rle arithmetic for Python. Docs here: https://biocore-ntnu.github.io/pyranges/turning-ranges-into-rles.html and here https://biocore-ntnu.github.io/pyranges/an-introduction-to-rles.html ...
written 6 months ago by endrebak800
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Comment: C: What do the positions '31776605 x 95917441' mean in GWAS catalogue data?
... Thanks! I did read the file format specification :) Strange it said nothing there. ...
written 6 months ago by endrebak800
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What do the positions '31776605 x 95917441' mean in GWAS catalogue data?
... 426 rows in the GWAS catalogue contain x in the CHR_POS, like '31776605 x 95917441' What does it mean? ...
gwas-catalogue written 6 months ago by endrebak800 • updated 6 months ago by Corentin450
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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 7 months ago by endrebak800

Latest awards to endrebak

Popular Question 5 weeks 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 10 weeks 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 4 months ago, created a question with more than 1,000 views. For Public paired end chip seq dataset, both ChIP and input?
Popular Question 5 months ago, created a question with more than 1,000 views. For Public paired end chip seq dataset, both ChIP and input?
Popular Question 5 months ago, created a question with more than 1,000 views. For Public paired end chip seq dataset, both ChIP and input?
Popular Question 5 months ago, created a question with more than 1,000 views. For Public paired end chip seq dataset, both ChIP and input?
Popular Question 8 months ago, created a question with more than 1,000 views. For Public paired end chip seq dataset, both ChIP and input?
Scholar 8 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
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How To Convert Gencode Gtf Into Bed Format ?
Popular Question 9 months ago, created a question with more than 1,000 views. For Public paired end chip seq dataset, both ChIP and input?
Appreciated 18 months ago, created a post with more than 5 votes. For Script to compute the effective genome size: epic-effective
Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For A: How To Convert Gencode Gtf Into Bed Format ?
Popular Question 18 months ago, created a question with more than 1,000 views. For Public paired end chip seq dataset, both ChIP and input?
Popular Question 18 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 18 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 18 months ago, created a question with more than 1,000 views. For Script to compute the effective genome size: epic-effective
Popular Question 18 months ago, created a question with more than 1,000 views. For How do I filter a bam on length with pybedtools?
Popular Question 18 months ago, created a question with more than 1,000 views. For Create bigwigs in python?
Centurion 19 months ago, created 100 posts.
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Script to compute the effective genome size: epic-effective
Popular Question 2.7 years ago, created a question with more than 1,000 views. For epic: new ChIP-Seq caller based on the SICER algorithm
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: How To Convert Gencode Gtf Into Bed Format ?
Voter 3.4 years ago, voted more than 100 times.

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