AUREAAn open-source software system for accurate and user-friendly identification of relative expression molecular signatures
DIRACDifferential Rank Conservation (DIRAC) provides quantitative measures of how network ordering differs within and between phenotypes.
GEMINIGene Expression and Metabolism Integrated for Network Inference (GEMINI)
ISSACIdentification of Structured Signatures and Classifiers (ISSAC) is a multiclass classification tool that can learn molecular signatures from high throughput gene expression data.
ITEPThe Integrated Toolkit for Exploration of Pan-genomes (ITEP) is a suite of scripts and Python libraries for the comparison of microbial genomes. It includes tools for de novo protein family prediction by clustering, ortholog detection, analysis of functional domains, identification of core and variable genes and gene regions, sequence alignments and tree generation, cluster curation, and the integration of cross-genome analysis and metabolic networks for study of metabolic network evolution.
Interstudy variabilityWe have assessed the influence of technical and biological sources of variability in transcriptomic data on predictive performance of molecular signatures learned from these data.
PROMProbabilistic Regulation of Metabolism (PROM) represents the successful integration of a genome scale transcriptional regulatory network with a biochemically detailed metabolic network, bridging two important classes of systems biology models that have rarely been combined quantitatively.
SNAPRA bioinformatics pipeline for efficient and accurate RNA-seq alignment and analysis
TSNWe have developed a new general formulation of the relative expression algorithm that is geared towards classification using small numbers of measured features (e.g. microRNAs). This is called the Top-Scoring 'N' algorithm (TSN), and it uses a flexible classifier size to expand the permutation and combination space available for classification.
TSP / TSTWe have implemented the relative expression classification algorithms the top-scoring pair (TSP) and top-scoring triplet (TST) for the graphics processing unit (GPU).
Integrative GBMCode(ipython notebooks), html files, data and figures for review of the analysis done for An Integrated Systems Approach to the Development of Molecular Signature of Biological Relevance for Glioblastoma.