User: endrebak
endrebak • 840
- Reputation:
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Posts by endrebak
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... 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 11 months ago by
endrebak • 840
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... Ah, I had no idea. That makes sense :) ...
written 11 months ago by
endrebak • 840
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... 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 11 months ago by
endrebak • 840
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... 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 ...
written 11 months ago by
endrebak • 840
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... 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. ...
written 13 months ago by
endrebak • 840
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... I would love to try to help you. Can you post an issue on the repo? ...
written 15 months ago by
endrebak • 840
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... 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 16 months ago by
endrebak • 840
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... Thanks! I did read the file format specification :) Strange it said nothing there. ...
written 17 months ago by
endrebak • 840
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240
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... 426 rows in the GWAS catalogue contain x in the CHR_POS, like '31776605 x 95917441'
What does it mean? ...
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... I know :) . I use it in my pyranges-library to write to bigwig: https://github.com/biocore-ntnu/pyranges ...
written 18 months ago by
endrebak • 840
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For How do I make a bigwig file from a matrix of counts?
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For A: Given a link that displays genome browser data, how do I download a pdf using a
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For How do I make a bigwig file from a matrix of counts?
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For Public paired end chip seq dataset, both ChIP and input?
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For Public paired end chip seq dataset, both ChIP and input?
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15 months ago,
created a question with more than 1,000 views.
For Public paired end chip seq dataset, both ChIP and input?
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15 months ago,
created a question with more than 1,000 views.
For Public paired end chip seq dataset, both ChIP and input?
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For Fast datastructure to get counts of overlapping reads per nucleotide (!) in Python?
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For Public paired end chip seq dataset, both ChIP and input?
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For A: How To Convert Gencode Gtf Into Bed Format ?
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19 months ago,
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For Public paired end chip seq dataset, both ChIP and input?
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For Script to compute the effective genome size: epic-effective
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For A: How To Convert Gencode Gtf Into Bed Format ?
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2.4 years ago,
created a question with more than 1,000 views.
For Public paired end chip seq dataset, both ChIP and input?
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2.4 years ago,
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For How do I make a bigwig file from a matrix of counts?
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2.4 years ago,
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For Different mappability/effective genome fraction with paired end reads? (ChIP-Seq)
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For Script to compute the effective genome size: epic-effective
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For Create bigwigs in python?
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For Script to compute the effective genome size: epic-effective
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For epic: new ChIP-Seq caller based on the SICER algorithm
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