User: dalloliogm

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dalloliogm40
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40
Status:
New User
Location:
European Union
Last seen:
1 year, 10 months ago
Joined:
2 years, 11 months ago
Email:
d*********@gmail.com

Posts by dalloliogm

<prev • 9 results • page 1 of 1 • next >
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AnnotationHub - Problem with SSL CA certificate
... I am trying to install AnnotationHub in a freshly installed Ubuntu system. I am getting some errors that seem to be related to missing libraries installed in the system. The first time I tried to install AnnotationHub I got some errors related to libcurl, but these were solved by installing libcurl ...
annotationhub dependencies written 23 months ago by dalloliogm40
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Comment: C: Can't load package "org.Hs.eg.db"
... the firewall is probably the cause, because the same URLs work for me. You can try a ping http://bioconductor.org/packages/3.1/bioc to see it the connection is blocked. Talk to your IT. ...
written 2.1 years ago by dalloliogm40
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Comment: C: How to find particular types of overlap with GenomicRanges
... Hi, sorry but your question is not really clear to me. From what I understand: hit1 overlap over the start position but not the end position; hit2 overlap over the end but not the start; hit3 overlap both start and end. Is it correct? I suspect you may use the resize function to get GRanges objects ...
written 2.1 years ago by dalloliogm40
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Comment: C: Can't load package "org.Hs.eg.db"
... For R 3.2 you may have to use a different url: install.packages("org.Hs.eg.db", repos="http://bioconductor.org/packages/3.2/bioc") ...
written 2.2 years ago by dalloliogm40
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getting the longest transcript by gene from Refseq
... The Refseq Gene table contains more than one transcript per gene: > library(dplyr) > library(AnnotationHub) > ahub = AnnotationHub() > refgene = ahub[['AH5040']] > table(table(mcols(refgene)['name'])) 1 2 3 4 5 6 7 8 9 10 12 13 19 4517 ...
annotationhub refseq written 2.2 years ago by dalloliogm40 • updated 2.2 years ago by Martin Morgan ♦♦ 20k
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Comment: C: Does AnnotationHub replaces AnnotationDbi for ID conversion (e.g. entrez, refseq
... Thank you, this is exactly what I wanted to know. I was surprised to see that the human OrgDb is not available, but I guess it will be introduced in the future. ...
written 2.2 years ago by dalloliogm40
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Does AnnotationHub replaces AnnotationDbi for ID conversion (e.g. entrez, refseq, symbols)?
... Hello, I am exploring the new AnnotationHub package and I find it fantastic. Thank you for all the effort, and also for the nice tutorials on coursera and youtube. I do not understand how much AnnotationHub will replace existing packages such as AnnotationDbi or the organism packages. For example ...
conversion symbol entrez written 2.2 years ago by dalloliogm40 • updated 2.2 years ago by James W. MacDonald45k
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Comment: C: Bioconductor on Coursera
... This is wonderful! Thank you very much for all this work. 1) Do you mind if I post this in Biostar? I am sure many people will be interested? 2) I think it will be good to have a lecture on ID conversion - e.g. from Entrez to Symbol, to RefSeq and so on. I am not sure if this is already explained ...
written 2.2 years ago by dalloliogm40
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Answer: A: ggbio error: Objects of type OrganismDb not supported by autoplot
... You must have loaded the package "ggplot2", which also contains a function called autoplot, so the ggbio functions got overwritten. To make sure that everything works properly, use ggbio::autoplot instead of autoplot. ...
written 3.0 years ago by dalloliogm40

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