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- SCAN.UPC. Single-channel array normalization (SCAN) and Universal exPression Codes (UPC) - A Bioconductor package.
- Gene Set Omic Analysis (GSOA). A tool for performing gene set analysis on multiple types of omic data.
- ShinyLearner. A software framework for performing benchmarks of machine-learning classification algorithms. It has a Web interface to facilitate the process of designing benchmarks.
- ToolJig. A simple approach to building Common Workflow Language tool descriptions and workflows.
- TidyGEO. A Web application that enables researchers to wrangle datasets from Gene Expression Omnibus.
- Good Nomen. A Web application that enables researchers to annotate tabular datasets with biomedical-ontology terms.
- Phlash. A Web application that facilitates gene annotation for bacteriophage genomes.