Gene Expression Data Normalization with data_norm

The program 'data_norm' normalizes gene expression data. It can be run from the command line and requires you to provide the input file, output file, and normalization method as arguments.

Here's a breakdown of its usage:

Usage:

data_norm -i input_file -o output_file -m normalization_method

Options:

• -i --input <input file>: Specifies the input file containing gene expression data.
• -o --output <output file>: Specifies the output file for the normalized data.
• -m --method <upqt | median | deseq | tmm | hkg>: Specifies the normalization method to use (default: upqt).
  • upqt: Uses upper quartile normalization.
  • median: Uses median normalization.
  • deseq: Uses DESeq normalization.
  • tmm: Uses TMM (trimmed mean of M-values) normalization.
  • hkg: Uses normalization based on a specific housekeeping gene list (only applicable with the --method hkg option).
• -g --gene <housekeeping gene list>: Specifies the list of housekeeping genes (required only for the --method hkg option).
• -v --version: Displays the GCEN version.
• -h --help: Prints help information.

Example:

data_norm -i ../sample_data/gene_expr.tsv -o ../sample_data/gene_expr_norm.tsv -m tmm

This command will normalize the gene expression data in the file 'gene_expr.tsv' using the TMM method and save the normalized results in the file 'gene_expr_norm.tsv'.