Rpadi_OrgDb

About the Database

The database has been updated! It now includes annotations performed using FANTASIA (12,698 genes assigned), patched with NCBI-specific annotations (351 genes assigned).

NOTE: FANTASIA tends to assign a gene to more GO terms, so the results may differ significantly from the previous NCBI-only annotations.

You can find the updated database and files at the following links:

Installation Instructions

Download and Install the OrgDb Database
First, download the .tar.gz file from the link above. After downloading, decompress the file (tar -zxvf org.Rpadi.eg.db.tar.gz) and install the database in R using the following command:
```
install.packages("PATH_TO/org.Rpadi.eg.db", repos = NULL, type = "source", force = TRUE)
```

Install clusterProfiler To use the clusterProfiler package, install it by running the following commands in R:

if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("clusterProfiler")

Example

Once the database and clusterProfiler are installed, you're ready to perform GO enrichment analysis. Below is an example:

library(clusterProfiler)
library(org.Rpadi.eg.db)

# Example gene list
genes <- c("LOC132916914", "LOC132916961", "LOC132917061", "LOC132917063", 
           "LOC132917180", "LOC132917253", "LOC132917261", "LOC132917313", 
           "LOC132917323")

# Perform GO enrichment analysis
go_results <- enrichGO(genes, keyType = "GID", OrgDb = "org.Rpadi.eg.db", ont = "ALL", pAdjustMethod = "BH")

# Visualize the results
dotplot(go_results)
barplot(go_results)