Interogates Bioconductor databases and identifies those that are compatible with Ularcirc. Builds a list of commands that the user can copy to install the required database on their local computer. Once installed the databases are immediately available to Ularcirc upon re-starting the shiny app. This function requires connection to the internet.
Compatible_Annotation_DBs(search_term = "")
: character string of a full or part name of a database. Will return only those entries that contain this search term. Not case sensitive.
Returns a list of compatible annotation databases
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# Get all Bioconductor annotation databases that are compatible with Ularcirc library('BSgenome') library('httpuv') library('AnnotationHub') # Prepare a dataframe of all compatible annotation databases ## Not run: compatible_DBs_human <- Compatible_Annotation_DBs("Hsapiens") # Example of how to find a relevant database and load the relevant databases: # This example find hg38 databases idx <- grep(pattern="hg38", x= compatible_DBs_human[,"genome"]) if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install(c(compatible_DBs[idx,])) ## End(Not run)
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