Substantial unannotated noncoding transcripts in tumors may transcriptionally regulate cancer-related genes

The CombatCorrected folder contains the cell line expression matrices and differential analysis results after ComBat batch effect correction. DEG_three_methods_function.R is the main script for differential analysis, containing three differential analysis methods: DESeq2, edgeR, and limma-voom. run_combat-DEanalysis.R is the script that calls this function, specifically designed for processing ComBat-corrected data. Tissues-DATA contains expression matrices and differential analysis results for tissue samples. The differential analysis method uses DEG_three_methods_function.R, without ComBat correction. Fasim-LongTarget repository, copied from https://github.com/LongTarget/Fasim-LongTarget