User: Dimitris Polychronopoulos

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50
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Location:
United Kingdom
Website:
http://group.genereg.n...
Twitter:
dpolychr2
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4 months, 1 week ago
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Posts by Dimitris Polychronopoulos

<prev • 21 results • page 1 of 3 • next >
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Answer: A: Plotting Differentially Methylated Regions
... You could also try the gtrellis bioconductor package; see example form DMR ...
written 11 months ago by Dimitris Polychronopoulos50
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Answer: A: M3D package in Bioconductor 3.4
... You could also try the following to see if they work for you: genomation::readBed genomation::readBroadPeak genomation::readNarrowPeak LOLA::readBed CNEr::readBed     ...
written 11 months ago by Dimitris Polychronopoulos50
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Given a multifasta file and for each sequence, shuffle middle part of the sequence leaving the flanks intact and the opposite
... Hi, I was wondering whether there is any function from a package in Bioconductor which, given a multiFASTA file and for each sequence, shuffles the middle part of the sequence leaving the flanks intact and the opposite? I guess "middle" and "flanks" have to be specified by the user. Thanks, Dimit ...
seqinr regioner shuffle written 11 months ago by Dimitris Polychronopoulos50 • updated 11 months ago by Martin Morgan ♦♦ 20k
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Comment: C: find next non-overlapping nth elements of a given region
... thank you! No, the genes have no strand information (strand = "*") ...
written 15 months ago by Dimitris Polychronopoulos50
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Comment: C: find next non-overlapping nth elements of a given region
... thanks Michael. When I apply this command for the mouse genes (as genes i have 19,369 GRanges with only the TSS as "start" and "end" position), I get 332,100 gene pairs. Would you think that this number makes sense?  ...
written 15 months ago by Dimitris Polychronopoulos50
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Comment: C: find next non-overlapping nth elements of a given region
... Thanks for the response, Michael. What I would like to get is all the possible gene-pairs within a window, let's say 500 kb. I thought of using findkNN (maybe try with a largest k, for instance 4 or 5), find the distances between genes constituting a gene - pair (based on their TSSs) and extract th ...
written 15 months ago by Dimitris Polychronopoulos50
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Comment: C: find next non-overlapping nth elements of a given region
... Dear Michael, Many thanks for the findkNN function. It has been proved very useful for my analysis as I was searching for a k-nearest neighbor finder for ranges for a long time. More specifically, I am trying to retrieve gene-pairs. What I have is a GRanges object (my.df.gr) containing external gen ...
written 15 months ago by Dimitris Polychronopoulos50
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Comment: C: closest-features equivalent in Bioconductor for finding closest gene(s)
... Thanks Michael for the suggestions, it worked! ...
written 19 months ago by Dimitris Polychronopoulos50
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Comment: C: closest-features equivalent in Bioconductor for finding closest gene(s)
... Thanks again, Michael. Maybe I miss something, but when I run this, it returns: total_DE_genes_gr$nearest_gene <- all_mouse_genes_gr[nearest(all_mouse_genes_gr)[match(total_DE_genes_gr, all_mouse_genes_gr)]] Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :   subscript con ...
written 19 months ago by Dimitris Polychronopoulos50
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Comment: C: closest-features equivalent in Bioconductor for finding closest gene(s)
... Many thanks Michael for your suggestion. I could not make it work,though, but I think i found a way using follow. More specifically: genes_index <- follow(total_DE_genes_gr,all_mouse_genes_gr,select=c("all")) #This gives me the second "best hit" nearest_genes <- all_mouse_genes_gr[subjectHit ...
written 19 months ago by Dimitris Polychronopoulos50

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Scholar 19 months ago, created an answer that has been accepted. For A: closest-features equivalent in Bioconductor for finding closest gene(s)

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