Provides access to a variety of QC metrics for assessing the quality of RNA samples and of the intermediate stages of sample preparation and hybridization. Simpleaffy also offers fast implementations of popular algorithms for generating expression summaries and detection calls. It is designed to work alongside the core ‘affy’ package from BioConductor and provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like.
A comprehensive collection of functions for conducting meta-analyses in R. The metafor package includes functions to calculate various effect sizes or outcome measures, fit fixed, random, and mixed-effects models to such data, carry out moderator and meta-regression analyses, and create various types of meta-analytical plots. For meta-analyses of binomial and person-time data, metafor also provides functions that implement specialized methods, including the Mantel-Haenszel method, Peto's method, and a variety of suitable generalized linear (mixed-effects) models (i.e., mixed-effects logistic and Poisson regression models).
This package performs aggregation of ordered lists based on the ranks using several different algorithms: Borda count, Cross-Entropy Monte Carlo algorithm, Genetic algorithm, and a brute force algorithm.
Provides a framework to perform Non-negative Matrix Factorization (NMF). NMF implements a set of already published algorithms and seeding methods. This method permits to test, develop and plug new/custom algorithms. The main interface function provides an easy way of performing parallel computations on multicore machines.
Permits exploration and integration of highly dimensional datasets. mixOmics proposes multivariate statistical approaches to identify similarities between two heterogeneous datasets. It summarizes information in a smaller data set and aims to highlight the biological entities that are of potential relevance with a strong focus on graphical representation. This tool assists in finding signatures of vaccine effect and allows a better understanding of immunological mechanisms activated by the intervention.
Enables systematic and effective capture of extensive experimental and clinical information with the highest minimum information about a microarray experiment (MIAME) score. MiMiR consists of an integrated platform for microarray data sharing, mining and analysis. It provides an environment for collection, capture, consistent annotation, visualization and dissemination of data. It contains over 3000 arrays worth of data for mining and analysis and supports over 200 research groups, including two international consortia.