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Sydney Bioinformatics and Biometrics

R

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 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. SoftwareJournal Article
DirectPA Identification of combinatorial effects due to multiple treatments or perturbations of pathways. SoftwareJournal Article
scClustBench Impact of similarity metrics on single-cell RNA-seq data clustering. SoftwareTBA

Shiny

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)