The software listed below is written in the R statistical programming language. It is open source and may be used without restrictions.
| Name | Brief Description | ||
| Variability Analysis of Networks (VAN) | VAN allows for the statistical testing of diferences in correlation between hub genes and their partners. | Software | Journal Article |
| ClassifyR | Framework for cross-validated classification and functionality to evaluate performance metrics (e.g. error rate) and draw plots of them. | Software | Journal Article |
| DCARS | A method for finding differential correlated genes across ranked samples. | Software | Journal Article |
| cellAggregator | A network method that simulates cell-cell aggregation assays. | Software | |
| MultiDA | A discriminant analysis classifier for use with high dimensional datasets which provides feature selection through multiple hypothesis testing. | Software | Preprint |
| blma | Averaging of linear models in a Bayesian framework. | Software | |
| VaDa | A family of Bayesian discriminant analysis models that performs within-model selection of discriminative variables and classification. | Software | |
| ClueR | Identification of the optimal number of clusters in a given time-course data set clustered by c-means or k-means algorithms. | Software | Journal Article |
| DirectPA | Identification of combinatorial effects due to multiple treatments or perturbations of pathways. | Software | Journal Article |
| scClust | scRNA-seq data clustering package, part of scdney R package, a suite of tools for scRNA-seq data analysis. | Software | Journal Article |
| scMerge | scMerge: Merging multiple batches of scRNA-seq data. | Software | Journal Article |
| scdney | Single cell data integrative analysis. | Software | |
The web applications run on a high performance server at University of Sydney.
| Name | Brief Description | ||
| PACMEN | A tool for exploring the relationships between mutations and gene expression changes in protein interaction subnetworks for 19 tissues analysed by TCGA. | Web Application | Journal Article |
| KinasePA | Enables analysis of kinase perturbation experiments. | Web Application | Journal Article |
| QPEP | A benchmarking scoreboard and visual analytics tools for methods which affect proteomics quantitation. | Web Application | Journal Article |
| QCMAP | Interactive quality control of mass spectrometry data processed by MaxQuant. | Web Application (GitHub) | Journal Article |