About

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
http://www.rennelab.com

Lead Developer

Changelog

  • 0.3.4 (2023-11) Changes include:

    • Misc Bugfixes and Refinements

    • Switch code linting to Ruff

    • Add hybkit.errors module and HybkitError classes

    • Moved printing of warnings to python logging module

    • Add option for direct passage of file-like object for construction of HybFile and ViennaFile

    • Add HybRecord.to_csv_header(), HybRecord.to_fields(), and HybRecord.to_fields_header() methods

    • Refine description of HybFile.open() constructor method

    • Add typing_extensions dependency

    • Add Python3.8-compatible type hints to API

    • Documentation Updates

  • 0.3.3 (2023-09) Changes include:

    • Misc Bugfixes and Refinements

    • Update integer bar-plot functions

  • 0.3.2 (2023-08) Changes include:

    • Misc Bugfixes and Refinements

    • Add duplicate hybrid filtration (by HybRecord.id) options to hyb_filter

    • Add duplicate hybrid filtration to example analyses

  • 0.3.1 (2023-08) Changes include:

    • Misc Bugfixes and Refinements

    • Add --version flag to scripts

    • Change move scripts output file description to argparse epilog

    • Refine plot functions

    • Change default plot colors to the Bang Wong scheme [Wong2011] for colorblind accessibility

    • Documentation corrections

    • Spellcheck

  • 0.3.0 (2023-04) Major Codebase And API Overhaul. Changes include:

    • Simplifying HybRecord API

    • Simplifying FoldRecord API

    • Unifying settings information for argparse and modules

    • Removing Support for ViennaD format

    • 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 within a single Analysis class

    • Added error checking / catching to HybFoldIter

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

    • Added "dynamic" seq_type to FoldRecord for non-identical fold/hybrid sequence handling

    • Added shell implementation to all example analyses

    • Remove support for Python3.6, Python3.7

    • Migrate to CircleCI for CI/CD

    • Added Pytest unit testing integrated with CircleCI

    • Other Misc. Improvements / Bugfixes

  • 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

References

ViennaFormat
ViennaRNA Vienna File Format Description
UNAFold Vienna File Format Description
CTFormat
UNAFold CT Format Description
RNAStructure CT Format Description
Zuker2003

Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003 Jul 1;31(13):3406-15. doi: 10.1093/nar/gkg595. PMID: 12824337; PMCID: PMC169194.

Hunter2007

J. Hunter, "Matplotlib: A 2D Graphics Environment" in Computing in Science & Engineering, vol. 9, no. 03, pp. 90-95, 2007. doi: 10.1109/MCSE.2007.55

Cock2009

Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, de Hoon MJ. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009 Jun 1;25(11):1422-3. doi: 10.1093/bioinformatics/btp163. Epub 2009 Mar 20. PMID: 19304878; PMCID: PMC2682512.

Lorenz2011

Lorenz, R., Bernhart, S.H., Höner zu Siederdissen, C. et al. ViennaRNA Package 2.0. Algorithms Mol Biol 6, 26 (2011). doi: 10.1186/1748-7188-6-26

Wong2011(1,2)

Wong, B. Points of view: Color blindness. Nat Methods 8, 441 (2011). doi: 10.1038/nmeth.1618

Helwak2013

Helwak A, Kudla G, Dudnakova T, Tollervey D. Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell. 2013 Apr 25;153(3):654-65. doi: 10.1016/j.cell.2013.03.043. PMID: 23622248; PMCID: PMC3650559.

Travis2014

Travis AJ, et al. Hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data. Methods. 2014 Feb;65(3):263-73. doi: 10.1016/j.ymeth.2013.10.015.

Gay2018

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.