BioXAK- preprocessed TCGA analysis data

This dataset contains preprocessed gene expression and clinical survival data derived from The Cancer Genome Atlas (TCGA), formatted specifically for use with BioXAK (Biology X Analysis Kit) — an open-source Windows desktop application for bioinformatics analysis designed for wet-lab researchers without programming expertise. Data Processing Pipeline Raw RNA-seq count data were downloaded from the GDC portal via the TCGAbiolinks R package, followed by variance-stabilizing normalization using DESeq2. Clinical survival information (days to last follow-up, vital status) was merged from GDC clinical metadata. The complete preprocessing R script is available in the BioXAK GitHub repository. File Format Each TCGA project is stored as two files: {PROJECT}_meta.json — Project metadata including gene IDs, sample IDs, sample conditions (tumor / normal), and per-sample clinical survival data. {PROJECT}_matrix.bin — DESeq2-normalized expression matrix stored as a little-endian 32-bit float binary array (genes × samples), enabling fast memory-mapped loading without text parsing overhead. A master index file projects_index.json lists all available projects with summary statistics (n_genes, n_samples, n_tumor, n_normal, survival availability). Cancer Types Included All available TCGA projects with sufficient samples were processed, including but not limited to: BLCA, BRCA, CESC, CHOL, COAD, ESCA, GBM, HNSC, KICH, KIRC, KIRP, LIHC, LUAD, LUSC, PAAD, PCPG, PRAD, READ, SARC, SKCM, STAD, THCA, THYM, UCEC. Intended Use These files are the data backend for BioXAK's TCGA Analysis module, which supports: Gene expression box plots across cancer types Heatmap clustering analysis Scatter plot and co-expression analysis Kaplan–Meier survival analysis with log-rank test Volcano plot for differential expression BioXAK automatically downloads this dataset on first launch if local data files are not detected. Source Data All raw data originate from TCGA via the NCI Genomic Data Commons (GDC). Per the TCGA data use policy , users of this dataset should acknowledge TCGA and GDC in any resulting publications. Software BioXAK source code and documentation: https://github.com/bowyung/BioXAK