The software listed below is written in the R statistical programming language. It is open source and may be used without restrictions.
|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||Preprint|
|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|
|scClustBench||Impact of similarity metrics on single-cell RNA-seq data clustering.||Software||TBA|
The web applications run on a high performance server at University of Sydney.
|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)|