Renne Lab

Principal Investigator: Rolf Renne
Henry E. Innes Professor of Cancer Research
University of Florida
UF Health Cancer Center
UF Department of Molecular Genetics and Microbiology
UF Genetics Institute

Lead Developer


  • 0.3.0a (ongoing) Major Codebase And API Overhaul. Changes include:

    • Simplifying HybRecord API

    • Simplifying FoldRecord API

    • Unifying settings information for argparse and module

    • Removing Support for ViennaD format

    • Addition of “NON” value to “target_reg” flag in specification

    • Moving identifier-parsing code to module type_finder

    • Moving target region analysis code to module region_finder

    • Moving code for settings into a “settings” module

    • Renamed HybRecord type_analysis and mirna_analysis to eval_types and eval_mirna, respectively to differentiate from analysis module functions

    • Reimplemented analyses methods as classes

    • Added error checking / catching to HybFoldIter

    • Removed Target-Region Analysis and associated files due to lack of archival database information, pending furure development

    • Added DynamicFoldRecord class for non-identical fold/hybrid sequence handling

    • Implemented hyb_analysis, hyb_exclude_fold, and hyb_fold_analysis executables

    • Added shell implementation to all example pipelines

    • Remove support for Python3.6

  • 0.2.0 (2020-03) Added Command-line Toolkit. Code Refinements.

  • 0.1.9 (2020-03) Fix for Module Path Finding for Python > 3.6

  • 0.1.8 (2020-03) Streamlining, PyPI / PIP Initial Release

  • 0.1.0 (2020-01) Initial Implementation



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Gay LA, Sethuraman S, Thomas M, Turner PC, Renne R. Modified Cross-Linking, Ligation, and Sequencing of Hybrids (qCLASH) Identifies Kaposi’s Sarcoma-Associated Herpesvirus MicroRNA Targets in Endothelial Cells. J Virol. 2018 Mar 28;92(8):e02138-17. doi: 10.1128/JVI.02138-17. PMID: 29386283; PMCID: PMC5874430.