User: Bosberg

gravatar for Bosberg
Bosberg30
Reputation:
30
Status:
New User
Location:
Germany, MPI
Last seen:
6 days, 3 hours ago
Joined:
1 year, 8 months ago
Email:
b******@dal.ca

bioinformatician and biophysicist based in Berlin.

Posts by Bosberg

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Pyranges: obtaining sets of overlaps or overlap pairs
... Original developper recommends `.join` . that is: pr1.join( pr2 ) and then one can index the resulting df by pr1 objects... ...
written 6 days ago by Bosberg30
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Comment: C: How to prevent reduce from being performed in GRanges during setdiff
... Thanks Rongxin. I added a few lines to make it a closed function to call above. ...
written 10 days ago by Bosberg30
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Answer: A: How to prevent reduce from being performed in GRanges during setdiff
... Thanks to Rongxin for putting me on the right track here. I wrote the following function in case anyone encounters this in the future: library(GenomicRanges) library(bedtoolsr) GRanges_subtract <- function( gr1, gr2 ) { # Subtract GRange object gr2 from gr1, but unlike ...
written 11 days ago by Bosberg30
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Pyranges: obtaining sets of overlaps or overlap pairs
... pyranges functions like overlap and intersect are great for selecting subsets of ranges that overlap, but I need to keep track of _which_ ranges overlap. I can think of two ways to accomplish this (they both have analogies to GRanges, and I'd be happy if I could find something in pyranges that does ...
list overlaps pyranges overlaps overlap pairs written 11 days ago by Bosberg30 • updated 11 days ago by Alex Reynolds31k
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Answer: A: Pyranges: operate on just metadata columns
... > Pyranges objects are dictionaries, where the keys are chromosomes (or tuples of chromosome & strand if a stranded object) and the values are pandas dataframes ... That was an excellently succinct and helpful first sentence that immediately cleared a lot of things up; Thank you! Btw, the d ...
written 12 days ago by Bosberg30
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Comment: A: How to change my email address
... Done. Thanks for the answer. This must create a lot of work for the admins, and I suppose there's some security/spam-flter reason for this, but if it can't be changed, I would recommend at least some kind of note on the "Edit your profile" just telling people "you cannot change your email address o ...
written 12 days ago by Bosberg30
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Forum: How to change my email address
... Incredibly basic question, but I cannot see how to change my email address on this forum. I've clicked on my account name --> "Edit your profile" and there I see how to change my username. However, it's my previous *email address* that is no longer valid. I've also searched for questions on this ...
email address account management forum change written 12 days ago by Bosberg30
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Pyranges: operate on just metadata columns
... In Granges there's a function mcol to access the columns describing various quantities under observation apart from the 'Canonical' position columns ( like "chrom", "start", "end" +optional "strand" etc. ). I'd like to try to access these entities in pyranges as well. For concreteness, take the foll ...
pyranges column selection pandas written 16 days ago by Bosberg30
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Comment: A: How to prevent reduce from being performed in GRanges during setdiff
... Apparently [PyRanges][1] does this by default with the function `subtract()` --which, I think is a much more logical default setting for something called 'subtract' (but for a function called 'setdiff()' I can understand this choice of default behavior; it would be nice if there were an equivalent ' ...
written 27 days ago by Bosberg30
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How to prevent reduce from being performed in GRanges during setdiff
... In the genomic ranges package for R, is there an option in `setdiff` that prevents the collapsing of adjacent ranges? for example, If I have the following: gr1 = GRanges object [1] chr1 1-10 * [2] chr1 11-20 * [3] chr1 21-30 * ...
setdiff blunt-end genomicranges written 28 days ago by Bosberg30

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