Compatible_Annotation_DBs {Ularcirc} | R Documentation

## 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
    compatible_DBs <- Compatible_Annotation_DBs()
    comatile_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[,"genome"])
    if (!requireNamespace("BiocManager", quietly=TRUE))
        install.packages("BiocManager")
    BiocManager::install(c(compatible_DBs[idx,]))

[Package Ularcirc version 1.0.0 Index]