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Databases, Data Systems Integration, Visualization & Exploration
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The Duke ICBP (DICBP) integrated Rb-E2F pathway database, pathway explorer and visualisation system
- DICBP provides the evolving representation of multiple forms of
genomic data, model/analysis summaries, and other information relevant to the integrated
understanding of the Rb-E2F pathways.
Go to the DICBP system using the DATABASE link above.
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DIG: Duke Integrated Genomics information system
- DIG provides a rich
source of data and tools for exploration of genomic information from experimental,
observational and literature sources. DIG includes advanced facilities for
PubMed searches on key words and phrases as well as graphical interrogation of
results using the GraphExplore software.
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GATHER: a systems approach to interpreting genomic signatures
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GATHER is a tool that integrates various forms of available data to elucidate biological context within molecular signatures produced from high-throughput post-genomic assays. It helps you understand the function of a group of genes, such as a cluster of co-regulated genes from microarrays.
Statistical Models for Gene Expression Studies
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BFRM: Bayesian Sparse Factor Analysis & Sparse Regression Modelling
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BFRM is a comprehensive implementation of sparse statistical models for high-dimensional data
including gene expression data coupled with outcomes (phenotypes) to be predicted based on
patterns underlying gene expression, and especially for biological pathway analysis and the evaluation
of subpathway structure.
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SSS: Shotgun Stochastic Search for regression variable search and uncertainty analysis
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SSS is an implementation of the shotgun stochastic search method for exploring and summarising subset regression models. Linear, binary and survival regression models are efficiently implemented for "large p" problems, with examples. Serial (Windows, linux/unix, 64bit linux) and parallel (linux cluster) code is available, with or without GUI facilities.
Modelling and Simulating Gene Circuits
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Dynetica: A Simulator of Dynamic Networks
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Dynetica provides a graphical construction of kinetic models of various biological systems, defined in terms
of components in the system and their interactions. The program automatically generates the ordinary differential equations,
time course simulations using either deteriministic algorithms or stochastic algorithms, and sensitivity analysis.
Exploring, Visualizing & Mining Graphical Genomic Structures and Data
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GraphExplore is a flexible system for management, display and
manipulation of network data, including facilities for visualisation and
interrogration of biological pathway and graphical model networks, and
interfaces to ontologies and searc facilities in DIG.
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CODENSE is a software package for mining coherent dense subgraphs from
multiple biological networks, and MODES,
designed for mining overlapping dense subgraphs in a large graph.
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NeMo (Network Module) is a software package to identify frequent dense vertex sets from multiple massive biological networks. It can be used to mine frequent co-expression modules across many microarray datasets.
Integrating Multiple Gene Expression Data Sets
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Integrative Array Analyzer (iArray) is a tool for integrative analysis of cross-platform
and cross-species microarray data.
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ChipMapper is a Matlab utility for mapping probe set IDs between Affymetrix chips U74Av2 and U95Av2, U133Plus and U95Av2.
Additional Statistical Tools for Gene Expression Profiling
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Profiler: Binary regression and metagene signature estimation for expression profiling
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Profiler has been developed for the identification of subsets of genes that together
underlie metagene patterns, or signatures, distinguishing outcomes based on a binary phenotype,
and underlies cancer genomic profiling and pathway characterisation in several ICBP related cancer
studies.
Image Analysis
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