markeR Shiny App Data

This dataset provides a comprehensive senescence compendium combining publicly available RNA-seq datasets, metadata, and curated gene sets for benchmarking and discovery of senescence-associated signatures. The record contains: counts.rds: Unprocessed RNA-seq data from the following public repositories: E-MTAB-5403, E-MTAB-9714, GSE175533, GSE60340, GSE63577, GSE64553, GSE214410, GSE222400, GSE224070, GSE230181, GSE235768, GSE247831, GSE74324, GSE75643, GSE94928, GSE130727, GSE250224, GSE196724, GSE206677, GSE217718, GSE110268, GSE213323, E-MTAB-10969. corrcounts.rds: Processed data, derived from the unprocessed datasets, filtered for lowly expressed genes, normalized, and batch-corrected, as described in the publication: https://www.biorxiv.org/content/10.64898/2025.12.05.692517 metadata.rds: Associated metadata describing experimental conditions, sample information, and other relevant annotations. SenescenceGeneSets.rds: Senescence gene sets included in the compendium: Empirically derived gene sets: SAUL_SEN_MAYO, CSGene, CellAge, SeneQuest, HernandezSegura. MSigDB gene sets: GOBP_CELLULAR_SENESCENCE, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_SENESCENCE, GOBP_POSITIVE_REGULATION_OF_CELLULAR_SENESCENCE, REACTOME_CELLULAR_SENESCENCE. Notes: All data are derived from publicly available sources. Users should cite both the original datasets and the markeR preprint when using this compendium. This repository is specifically made available to support the development and demonstration of a Shiny application for markeR.