sk-sahu / sig-bio-shiny Goto Github PK
View Code? Open in Web Editor NEWA standalone interactive application for detecting biological significance on a set of genes
Home Page: http://sk-sahu.github.io/sig-bio-shiny
License: MIT License
A standalone interactive application for detecting biological significance on a set of genes
Home Page: http://sk-sahu.github.io/sig-bio-shiny
License: MIT License
For now, this requires at least 8GB memory to run few clusterProfiler functions.
Someway if this can hold to a lesser memory.
When a enrich function returns NULL
the app disconnected
No gene set have size > 10 ...
--> return NULL...
When the input list and gene-id type doesn't match shiny app disconnection.
Error: Failed to install 'SigBio' from GitHub:
Failed to install 'DOSE' from GitHub:
(converted from warning) cannot remove prior installation of package ‘backports’
Once the input IDs detected it can be used to
The RStudio example seems to crash when I try testing it. When downloading and trying this locally I ran into several issues with dependencies such as rlang
, which required manual updating:
> runApp('sig-bio-shiny-app.R')
Running Sig-Bio-Shiny v0.2.3 | Sun May 17 14:47:47 2020
Checking if SigBio v0.2.3 Package is installed...
Error: package or namespace load failed for ‘SigBio’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
namespace ‘rlang’ 0.4.5 is already loaded, but >= 0.4.6 is required
> install.packages("rlang")
Once this was resolved, I used 'Run app' to run the application per the instructions, but ran into the below. Intermittent issues with KEGG availability?
Info: Downloading xml files for NA, 1/0 pathways..
Warning in download.file(xml.url, xml.target, quiet = T) :
cannot open URL 'http://rest.kegg.jp/get/NA/kgml': HTTP status was '400 Bad Request'
Warning: Download of NA xml file failed!
This pathway may not exist!
Info:
Warning:
Info: Downloading png files for NA, 1/0 pathways..
Warning: Download of NA png file failed!
This pathway may not exist!
Info:
Warning:
Warning: Failed to download KEGG xml/png files, hsa skipped!
Use this - shinymeta
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