Workflow scriptsRNA, totalRNA, smallRNA, and integration scripts and input files. A short README briefly describes scripts and their execution.
The SePIA workflow and target prediction database used are available for download here. For convenience, a list of publically available TCGA samples, a link to the GEO dataset, annotation files and resources used in this study are provided.
Resources and annotations
The SePIA workflow and target prediction database created and used for the case studies are available for download here.
- mirTPdb - SQLite database of predicted and validated miRNA targets used in the paper. See the mirTPdb_resources.csv file in the scripts for database breakdown.
- mirTPdb input files - formatted list of predicted and validated miRNA-target pairs downloaded from cited sources and used to create the SQLite database.
- SePIA resources - Human annotation files (NCBI38), references, STAR resources, and executable libraries (DEXSeq, Bambino, RNA-SeQC_v1.1.8) used in the case studies.
- All functions and components available for use with the SePIA workflow can be referenced in the Anduril documentation.
Case studiesTCGA sequenced breast cancer samples used in the case study are listed as follows:
Result reportsOutput generated by the SePIA demo run in Docker.
- DEMO output - 'raw' results from the demo execution of smallRNA-pipeline.and
- DEMO report output - the same results reorganized and given descriptive text for more informed browsing, generated by exection of smallRNA-report.and.