Compatible_Annotation_DBs: Compatible_Annotation_DBs

In VCCRI/Ularcirc: Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)

Compatible_Annotation_DBs

Description

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.

Usage

Compatible_Annotation_DBs(search_term = "")

Arguments

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.

Value

Returns a list of compatible annotation databases

Examples

# 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)

VCCRI/Ularcirc documentation built on April 8, 2022, 5:17 p.m.