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RIPSeeker viewRIP function fails to extract values() in GRangesList/S4 object

s4 ripseq rip values() written 2.9 years ago by CrisMar • 80

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How to efficiently reuse and optimize same code block in wrapper function?

R s4 sequence written 4.2 years ago by Jurat Shahidin • 80 • updated 4.2 years ago by Santosh Anand ♦ 5.2k

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Recent Replies

C: Download entire human rRNA sequences by dare_devil • 1.3k
Look at this [paper][1] [1]: https://academic.oup.com/nar/article/39/12/4949/2411105
A: Setup PHG with Singularity by petinho86 • 0
Hi Zack, Yes singularity has nothing to do with this. It looks like it all stands and falls with...
C: List of TCGA genes differentially expressed in normal versus tumor by a.james • 210
there is no option to download the differentially expressed genes
C: Do read group names have effect on marking duplicates using GATK? by Kevin Blighe ♦ 69k
If no answer here, you may consider asking on the GATK Support Forum, which, I assume, caters als...
C: What is index in sortmerna? by GenoMax ♦ 95k
Ah I see. You used `folder containing input fasta file` as an indicator that you have a real valu...
A: is there any solution to convert a multifasta file to csv? by Mensur Dlakic • 8.4k
This should get you going: from Bio import SeqIO for re in SeqIO.parse('CHIKV1-X-gb_AB45...
C: Annotate PBMC scRNA-seq data by yzhao140 • 0
Thank you very much! I will have a try.
C: is there any solution to convert a multifasta file to csv? by _r_am ♦ 32k
You're halfway there. `re.id + redescription` should give you the whole header, make sure of that...
C: is there any solution to convert a fasta file to csv? by projetoic • 0
Multifasta - with many sequences fasta. I'm going to edit sorry. Is there any solution?
A: limma goana or kegg by Gordon Smyth • 2.1k
See ?goana. The input to goana is pretty straightforward. Just read the documentation, no need to...
A: GO annotation goana by Gordon Smyth • 2.1k
Just make two vectors of up and down DE genes, then ``` goana(list(Up=IDs.up,Down=IDs.down), spe...
C: What is index in sortmerna? by taufiqbge • 0
Thanks for your reply. I checked the (,) and also went through the manual. I just mentioned "fold...

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