Gene Conversion and Annotation Scripts

This repository contains three R scripts for gene-related data conversion and annotation. These scripts are designed to provide a convenient way to convert gene identifiers and retrieve additional information from public databases.

Scripts

1. ACCNUM_to_SYMBOL.r

This script takes a file containing ACCNUM IDs and converts them to gene symbol names using the org.Hs.eg.db package. It is particularly useful for gene expression data processing.

Usage

Rscript ACCNUM_to_SYMBOL.r input_file.txt output_file.csv

Example data downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52530 GSE52530_HeLa.expData.txt.gz

2. ENSEMBL_to_SYMBOL.r

This script reads a file with ENSEMBL IDs and converts them to gene symbol names using the org.Hs.eg.db package. It is designed to facilitate the translation of ENSEMBL IDs to more interpretable gene symbols.

Usage

Rscript ENSEMBL_to_SYMBOL.r input_file.txt output_file.csv

Example data downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE149204 GSE149204_Nanopore_sequencing_readcounts.txt.gz

3. genetype_ensembl.r

This script utilizes the biomaRt package to convert gene symbols into Ensembl IDs and retrieve corresponding gene biotypes. It provides information on the types of genes based on Ensembl IDs.

Usage

Rscript genetype_ensembl.r input_file.csv output_file.csv

Prerequisites

Make sure to install the required R packages before running the scripts. The scripts use BiocManager, org.Hs.eg.db, AnnotationDbi, and biomaRt.

# Install BiocManager if not already installed
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.15")

# Install required packages
BiocManager::install(c("org.Hs.eg.db", "AnnotationDbi", "biomaRt"))