Inflammatory bowel diseases (IBD) gene expression data for the manuscript entitled "Supervised Ensemble Learning Identifies Minimal Consensus Gene Signatures for Crohn's Disease Classification"

RNA sequencing reads related to IBD intestinal biopsies were obtained from the Sequence Read Archive (SRA). All samples were uniformly processed using a standardized custom pipeline to ensure consistency across datasets. Quality control was performed with fastp (v1.0.1), followed by alignment to the human reference genome GRCh38.p14 (NCBI RefSeq assembly GCF_000001405.40) using STAR (v2.7.10) with default parameters. Read strandedness was assessed with RSeQC (v5.0.1), and transcript quantification was carried out using Rsubread (v2.22.1). Publicly available datasets included in this repository: PRJNA248469, PRJNA565216, PRJNA702434, PRJNA728646, PRJNA985602. ibd_counts.csv – contains gene expression count data from all included studies. To avoid non-interpretable results and reduce computation time, genes not annotated in GO or KEGG were filtered out from this table. ibd_clin.csv – contains clinical metadata for all samples across all studies. ibd_dataset.Rdata - contains both tables in a single .Rdata object. TENTACLES_Workflow.html - contains a demonstration vignette that shows how to work with TENTACLES. ibd_dataset.Rdata is used for this demonstration.