Registered 2006-09-12 by Ramon Diaz-Uriarte

A tool for finding differentially expressed genes, and genes that are of potential interest because they are related to an outcome of interest (e.g., type of cancer, survival) in analysis of microarray data. Includes correction for multiple testing.

A tool for the analysis of microarray data to find differentially expressed genes related to class differences (e.g., cancer vs. non-cancer), survival data, and continuous data (e.g., regression of protein concentration on gene expression). Also useful for tissue array data (e.g., Fisher's test).

Available tests: permutation-based (Anova, t, regression), linear models (with empirical bayes moderation), including option to adjust for additional covariates (e.g., sex, age), survival analysis (Cox model), Fisher's exact test for IxJ contingency tables.

Output includes adjustable heatmaps with dendrograms, links to additional functional/bibliographic information, and Venn diagrams of subsets of genes.

Mosts computations are parallelized (MPI) allowing for extremely fast operation on our 60-CPUs computing cluster.

Project information

Part of:
Asterias Project
Maintainer:
Ramon Diaz-Uriarte
Driver:
Not yet selected
Licence:
GNU Affero GPL v3, GNU GPL v2, GNU GPL v3

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trunk series is the current focus of development.

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Version control system:
Bazaar
Programming languages:
Python, R, C++

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