TRuST: LINCS Backend Resource for Transcriptomic Signature-Driven Drug Repurposing

This dataset contains processed backend resources derived from the LINCS L1000 perturbational signature resource distributed through Bioconductor ExperimentHub (EH3226). The resource was prepared to support the deployment and reproducible use of TRuST (Transcriptomic Repurposing Signature web Tool), a Shiny-based framework developed for transcriptomic signature-driven drug repurposing analysis. Version 2.0.0 introduces a chunked backend architecture designed to reduce memory and storage requirements during deployment and analysis. Instead of relying on a single large backend file, the LINCS signature matrix is partitioned into 90 RDS chunks. A gene-to-chunk index enables TRuST to identify and load only the chunks containing genes required for a given query, thereby avoiding unnecessary loading of the complete LINCS resource. The v2.0.0 backend contains: 90 chunked RDS files containing the processed LINCS signature matrix; gene_chunk_index.rds, providing gene-to-chunk and local-row indexing; signature_names.rds, containing the signature metadata; manifest.rds, describing the backend structure and number of chunks. The backend was generated by retrieving the original LINCS resource through Bioconductor ExperimentHub, validating the underlying SummarizedExperiment object, extracting and cleaning the expression matrix, removing missing and duplicated gene identifiers, and generating indexed chunks for efficient signature retrieval. The chunked architecture allows TRuST to retrieve only the backend components required by a query. This is particularly important for deployment on environments with limited memory or storage resources and supports more scalable and reproducible use of the application. The original LINCS L1000 data are publicly available through the LINCS consortium and Bioconductor resources. This Zenodo record contains processed derivative resources generated for computational optimization, reproducible deployment, and integration within the TRuST framework. The original data ownership and licensing conditions remain with their respective providers. Version 2.0.0 supersedes the monolithic backend distribution provided in Version 1.0.0 and is intended for use with the corresponding v2.x TRuST application.