Software
Many of our tools are publicly available and can be explored from this page. Open source software can be found at CCICB on GitHub and CCIACB on Bitbucket. If you’d like to learn more about any of our tools, please get in touch via our contact form.
Publicly Accessible Tools
Cancer Cohort
A cancer cohort data analysis platform.
R
Sam El-Kamand
Published in NAR Genomics & Bioinformatics (2024) PMID: 38304083
Germline WGS
Database of >50,000 variants with functional evidence for altering splicing.
Online Tool
Patricia Sullivan
Published in AJHG (2024) PMID: 39226898, DOI: 10.1016/j.ajhg.2024.08.002
Data Sharing
A GA4GH (v2) Beacon for sharing human genome data from the ZERO Program.
Online Tool
Data Sharing
A proof of concept Australian federated data sharing portal using the GA4GH Beacon (v2) protocol, hosted by Australian BioCommons.
Online Tool
Cancer WGS
Cancer WGS
Simplifies the evaluation, exploration, and visualisation of mutational signatures in R.
R
Sam El-Kamand
Cancer WGS
Identify Radiation Induced Glioma (RIG) signatures by analysing gene expression data.
R
Cancer WGS
A molecular curation portal for the analysis, interpretation, and reporting of precision medicine data from the ZERO program.
Online Tool
ZEROmutations
Cancer WGS
R package for analysing childhood cancer data from the ZERO program (available under data access agreement).
R
Cancer WGS
R packages for analysing adult cancer whole genome data cancer cohorts from PCAWG.
R
Cancer WGS
R packages for analysing adult cancer Somatic Copy Number alterations from the TCGA project.
R
Germline WGS
Germline WGS
Introme prioritises coding and noncoding splice-altering variants for clinical variant interpretation.
Python
Published in Genome Biology (2023) PMID: 37198692
Germline WGS
Clinical grade structural and copy number variant detection from whole genome sequencing data.
R
Published in Genome Medicine (2021) PMID 33632298
Germline WGS
A comprehensive web platform for storing and interrogating human genomic variation.
Online Tool
Published in Bioinformatics (2018)
PMID 32499604
Germline WGS
A Highly Sensitive Mitochondrial Variant Analysis Pipeline for Whole Genome Sequencing Data.
PythoN
PublisheD in J Bioinform Syst Biol 7 (2024) doi:10.26502/jbsb.5107074
Sabretooth
Germline WGS
Germline WGS analysis of short variants (SNVs and indels). Used to analyse >10,000 human WGS samples as part of the Garvan Institute Sequencing Platform.
Internal Tool
Cancer RNA
Carbonite
Cancer RNA
Comprehensive tumour RNA-seq analysis pipeline with structural variant detection, used in real-time to analyse patients recruited onto the ZERO program.
Internal Tool
Mayoh et al, in prep
Cancer RNA
Gene expression classifier of T-cell inflamed tumours.
R
Published in Genome Medicine (2023)
doi:10.1186/s13073-023-01170-x
Cancer Cohort
Cancer Cohort
A shiny dashboard for building virtual gene panels from cancer variants prioritisation.
R, Shiny
Cancer Cohort
Database of genes which frequently sustain somatic mutations, but are unlikely to drive cancer.
R
PINA v2.0
Cancer Cohort
A web-based tool for mining protein-protein interactome modules.
Online Tool
Published Nucleic Acids Res (2012)
PMCID PMC3244997
Cancer Epigenetics
Methyliser
Cancer Epigenetics
Tool for providing visualisations for the methylation status of genes.
R
Mayoh et al, in prep
Data Sharing
Data Sharing
An open-source user interface for GA4GH Beacon (v2) that can be deployed to create your own Beacon Network.