User: sergi.picart

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sergi.picart20
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Posts by sergi.picart

<prev • 10 results • page 1 of 1 • next >
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Answer: A: 404 Not Found error in FELLA
... A fix has been pushed, so it should be available soon. KEGG still keeps organism-specific modules, but not within `keggList()`. Now organism-specific modules are determined by imposing that at least one organismal gene must lie within them. Some small tests on `hsa` and `sce` suggest that this shoul ...
written 7 weeks ago by sergi.picart20
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404 Not Found error in FELLA
... I have received several inquiries about a recent error in FELLA. The message, after calling **buildGraphFromKEGGREST**, looks like the following: Error in .getUrl(url, .listParser, nameColumn = 1, valueColumn = 2) : Not Found (HTTP 404) This is due to our dependency KEGGREST, so we ...
software error fella written 9 weeks ago by sergi.picart20
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Answer: A: FELLA package - How to obtain the KEGG IDs that mapped to a pathway
... Dear Cecilia, There is no "nice" built-in way to solve your query, but it is indeed possible to get around it. I have attached a script - hope it helps. # example on how to extract individual metabolite hits in hypergeom library(igraph) library(FELLA) library(plyr) library(dp ...
written 8 months ago by sergi.picart20
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Comment: C: FELLA package - How to obtain the KEGG IDs that mapped to a pathway
... Edit: provided answer instead of comment ...
written 8 months ago by sergi.picart20
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Answer: A: Trouble installing GOSemSim
... The solution was to run `BiocManager::valid()` to spot outdated packages, thanks to Lluís and shepherl. The same command also suggests a call to `BiocManager::install` with the names of such packages (see comments). Afterwards, `BiocManager::install("GOSemSim")` did the trick. ...
written 8 months ago by sergi.picart20
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Comment: C: Trouble installing GOSemSim
... It's working now - thank you very much for a prompt and precise help! I ran the following chunk: BiocManager::install(c( "AER", "affy", "affyio", "AnnotationDbi", "BH", "BiocGenerics", "BiocInstaller", "bit", "bootstrap", "couchDB", "curl", "data.table", "devtools", "d ...
written 8 months ago by sergi.picart20
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Comment: C: Trouble installing GOSemSim
... This is the output. I will try to update the out-of-date packages > BiocManager::valid() * sessionInfo() R version 3.5.2 (2018-12-20) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.2 LTS Matrix products: default BLAS: /usr/lib/x86_64 ...
written 8 months ago by sergi.picart20
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Comment: C: Trouble installing GOSemSim
... Yes, it is already in its latest version `0.20.1` (https://bioconductor.org/packages/release/bioc/html/S4Vectors.html) ...
written 8 months ago by sergi.picart20
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Trouble installing GOSemSim
... When I try to install GOSemSim I get the following error with S4Vectors > BiocManager::install("GOSemSim") Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.2 (2018-12-20) Installing package(s) 'GOSemSim' trying URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/GOSem ...
gosemsim s4vectors written 8 months ago by sergi.picart20
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Answer: A: consulting about the FELLA package
... Hello, First of all, thank you for using our tool - we highly appreacite it. About your issue, you can fix it by taking the sub-graph as an igraph object and use its plotting arguments. You can play with pretty much every graphical attribute, I have attached an example. # example on how to ...
written 10 months ago by sergi.picart20

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