User: Jurat Shahidin
Jurat Shahidin • 60
- Reputation:
- 60
- Status:
- Trusted
- Location:
- Italy
- Website:
- http://home.deib.polim...
- Last seen:
- 8 months, 2 weeks ago
- Joined:
- 3 years ago
- Email:
- j********@gmail.com
Posts by Jurat Shahidin
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... 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 ...
written 15 months ago by
Jurat Shahidin • 60
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... @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 22 months ago by
Jurat Shahidin • 60
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... @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?
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written 22 months ago by
Jurat Shahidin • 60
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... 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 ...
written 22 months ago by
Jurat Shahidin • 60
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... Dear Mike:
Thanks for your effort. I figured out the problem.
Best regards:
Jurat
...
written 24 months ago by
Jurat Shahidin • 60
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... 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 24 months ago by
Jurat Shahidin • 60
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... 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 ...
written 24 months ago by
Jurat Shahidin • 60
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... Dear Martin :
I figured out issue. Thanks a lot for your idea on this problem.
Best regards :
Jurat
...
written 2.0 years ago by
Jurat Shahidin • 60
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... @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 2.0 years ago by
Jurat Shahidin • 60
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... @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 2.0 years ago by
Jurat Shahidin • 60
Latest awards to Jurat Shahidin
Popular Question
19 months ago,
created a question with more than 1,000 views.
For Find overlap for more than 2 GRanges object simultaneously (reproducible example is updated) ?
Popular Question
19 months ago,
created a question with more than 1,000 views.
For Find overlap for more than 2 GRanges object simultaneously (reproducible example is updated) ?
Popular Question
22 months ago,
created a question with more than 1,000 views.
For Find overlap for more than 2 GRanges object simultaneously (reproducible example is updated) ?
Scholar
2.7 years ago,
created an answer that has been accepted.
For A: How to sort set of GRanges object in the list by increasing order?
Voter
2.7 years ago,
voted more than 100 times.
Centurion
2.7 years ago,
created 100 posts.
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For Couldn't install GenomicRanges packages after update bioconductor to 3.2 version ?
Scholar
2.7 years 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
2.7 years ago,
created an answer that has been accepted.
For A: How to conditionally combine IntegerList in the DataFrame more elegantly?
Scholar
2.7 years ago,
created an answer that has been accepted.
For A: How to avoid repeated overlap pair for GRanges object in grid?
Student
2.8 years ago,
asked a question with at least 3 up-votes.
For Find overlap for more than 2 GRanges object simultaneously (reproducible example is updated) ?
Rising Star
2.9 years ago,
created 50 posts within first three months of joining.
Supporter
2.9 years ago,
voted at least 25 times.
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