Software
The following open source projects have either been designed by or had significant input into their design and implementation from Melbourne Bioinformatics experts.
| Name | Description | Link |
|---|---|---|
| Bioinitio | A template for command line bioinformatics tools in various programming languages. The purpose of the tool is to provide an easy-to-understand working example that is built on best-practice software engineering principles. It can be used as a basis for learning and as a solid foundation for starting new projects. Published in Gigascience, 2019. | Bionitio |
| Bpipe | A bioinformatics pipeline. Published in Bioinformatics, 2012. Collaboration with Murdoch Children’s Research Institute. | Bpipe |
| Degust | A web tool to help analyse, visualise and fully appreciate Differential Gene Expression data from RNA-seq experiments. Collaboration with VBC, Monash University. | Degust |
| Dovex | A web based tool to quickly provide an interactive overview and enable quick exploration of datasets. | Dovex |
| Gurita | A command line tool for analysing and visualising tabular data in CSV or TSV format. | Gurita |
| Janis | A framework for creating specialised, simple workflow definitions that are then transpiled to Common Workflow Language or Workflow Definition Language. Developed as part of the Portable Pipelines Project, a collaboration with Peter MacCallum Cancer Centre and WEHI. | Janis |
| sEst | An R-package for estimating sex from DNA methylation microarray data | sEst |
| SRST2 | Short Read Sequence Typing for Bacterial Pathogens. Published in Genome Medicine, 2014. Collaboration with Prof Kat Holt (Monash University) and Prof Mike Inouye (Baker Institute). | SRST2 |
| TotalPerspectiveVortex | Provides an installable set of dynamic rules for the Galaxy application that can route entities (Tools, Users, Roles) to appropriate destinations based on a configurable yaml file. | TotalPerspectiveVortex |
| Varlap | A tool aimed at quality control of DNA variants arising from sequencing alignments. | Varlap |