Adjusting batch effects in microarray expression data using Empirical Bayes methods. The modified ComBat (M-Combat) is designed specifically in the context of meta-analysis and batch effect adjustment for use with predictive models that are validated and fixed on historical data from a ‘gold-standard’ batch.
Contains functions for the storage, management and analysis of oligonucleotide arrays. affy provides the user with extreme flexibility when carrying out an analysis and make it possible to access and manipulate probe intensity data. The affy package was designed to balance user control of data analysis with convenience. Graphical user interfaces, object oriented programming and modular function design enhance the convenience of the package.
Provides statistical tools for visualization and analysis of microarrays. GeneSpring GX offers an interactive environment that promotes investigation and enables understanding of Transcriptomics, Genomics, Metabolomics and Proteomics data within a biological context. It can be used for expression arrays, miRNA, exon arrays and genomics copy number data. It also allows to identify targets of interest that are both statistically and biologically meaningful.
Serves for the functional analysis of gene expression and genomic data. Babelomics offers the possibility to explore the effects of alteration in gene expression levels or changes in genes sequences within a functional context. It provides user-friendly access to a full range of methods that cover: (1) primary data analysis; (2) a variety of tests for different experimental designs; and (3) different enrichment and network analysis algorithms for the interpretation of the results of such tests in the proper functional context.
Offers an intuitive user interface and built-in workflows for a variety of genomic applications that guide researchers though every step of the analysis process. Partek Genomics Suite gives biologists, bioinformaticists, and statisticians a single, integrated solution for trustworthy results with a user-friendly interface, comprehensive workflows, and ability to support all next generation sequencing, microarray, and qPCR platforms.
Implements a unified framework for preprocessing microarray data and interfaces with other BioConductor tools for downstream analysis. The Oligo package provides array coordinates, feature types, sequences, feature names and other relevant information for preprocessing. Developers can use oligo solutions to facilitate the integration of their tools with BioConductor. They also benefit from the unified model that the package makes available, as the consistency in data delivery and handling improves efficiency.
A package to analyze small to extremely large Affymetrix datasets. Aroma.affymetrix allows to analyze any number of arrays of various chip types, e.g. 10,000s of expression arrays, SNP chips, exon arrays and so on. This software does not require any normalisation step and does not summarise the probe intensities.