User: Jurat Shahidin

Reputation:
60
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Trusted
Location:
Italy
Website:
http://home.deib.polim...
Last seen:
3 weeks ago
Joined:
1 year, 11 months ago
Email:
j********@gmail.com

Posts by Jurat Shahidin

<prev • 113 results • page 1 of 12 • next >
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Seeking bioconductor package or alternative hand-on tools to carry out phylogenetic analysis
... Dear All: I am looking for bioconductor packages or alternative hand-on software tools to carry out phylogenetic analysis. I aware that Geneious (https://www.geneious.com/ ) provide abundant features to perform phylogenetic analysis, but it is not free for academic research. I believe Bioconductor ...
ngs phylogenetic software tools written 9 weeks ago by Jurat Shahidin60
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Comment: C: How to render summary list for `GRangesList` by using `SummarizedExperiment` pac
... @Vincent: Dear vincent, the problem I faced is printing out GRangesList is not favorable for me, while rendering summary of each GRanges would be good option aims to give clear output for the user, that's why I am trying to find the easy workaround for this problem. Hope you will direct me some usef ...
written 9 months ago by Jurat Shahidin60
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Comment: C: How to render summary list for `GRangesList` by using `SummarizedExperiment` pac
... @Vincent: Dear Vincent, thanks for your help. BTW, I am expecting rather simple, intuitive solution to achieve my goal. What if I first flatten out GRangesList as one common GRanges, then use SummarizedExperiment package to render simple statistics? Is that workable? ...
written 9 months ago by Jurat Shahidin60
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How to render summary list for `GRangesList` by using `SummarizedExperiment` package?
... Hi: Given processed ChIP-Seq peaks in `GRangesList`, I want to use the functions from `SummarizedExperiment` package to render succinct summary output. However, I looked into package vignette and tried to learn how to use this on `GRangesList`. My goal is, based on `GRangesList`, I want to let R pr ...
grangeslist R summarizedexperiment written 9 months ago by Jurat Shahidin60
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Comment: C: do.call error "second argument must be a list" with GRanges object
... Dear Mike: Thanks for your effort. I figured out the problem. Best regards: Jurat ...
written 10 months ago by Jurat Shahidin60
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Comment: C: do.call error "second argument must be a list" with GRanges object
... Dear Mike: Yes, resGR was generated as GRanges which contains a subset of ranges in grs (where the order of ranges was different). Yes, I want back resGR as GRangesList. resGR has fewer ranges because some of the ranges were filtered out by a threshold. Why my solution won't work with S4 class? Is ...
written 10 months ago by Jurat Shahidin60
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do.call error "second argument must be a list" with GRanges object [closed]
... Hi : I have GRangesList grs to find overlap and other meta-analyses, after several workflows, I obtained resGR, which needed to be relisted. However, I come up with the solution to relist `resGR` as GRangesList, but I got an error. My solution works fine with data.frame, but can't work with the S4 ...
R error handling written 10 months ago by Jurat Shahidin60
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Comment: C: Any way to proceed duplicate removal for list of GRanges object ?
... Dear Martin : I figured out issue. Thanks a lot for your idea on this problem. Best regards : Jurat ...
written 11 months ago by Jurat Shahidin60
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Comment: C: Any way to proceed duplicate removal for list of GRanges object ?
... @Can Hi Can, you can edit your answer by deleting grl, grl_expect, only keep the code that what you've done. I liked your idea of solving this problem, thank you. But, making your code's body smaller, smarter is always helpful for others to learn your approach. Yes, data.table package provides some ...
written 11 months ago by Jurat Shahidin60
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Comment: C: Any way to proceed duplicate removal for list of GRanges object ?
... @Martin Dear Martin Thanks for your insightful answer. Regarding the part of getting index list keep, Any idea to make this part more programmatic and prettier ? ...
written 11 months ago by Jurat Shahidin60

Latest awards to Jurat Shahidin

Scholar 19 months ago, created an answer that has been accepted. For A: How to avoid repeated overlap pair for GRanges object in grid?
Scholar 19 months ago, created an answer that has been accepted. For A: How to sort set of GRanges object in the list by increasing order?
Scholar 19 months ago, created an answer that has been accepted. For A: How can I get global Fisher score for overlap of 3 GRanges object by element-wis
Scholar 19 months ago, created an answer that has been accepted. For A: How to conditionally combine IntegerList in the DataFrame more elegantly?
Voter 19 months ago, voted more than 100 times.
Centurion 19 months ago, created 100 posts.
Popular Question 19 months ago, created a question with more than 1,000 views. For Couldn't install GenomicRanges packages after update bioconductor to 3.2 version ?
Rising Star 21 months ago, created 50 posts within first three months of joining.
Supporter 22 months ago, voted at least 25 times.

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