Allows users to collect, manage, and effectively analyze data from microarray experiments. TM4 Microarray Software Suite is composed of a set of four tools: Madam, Spotfinder, Midas and MeV. It offers functions that allow users to record their experimental parameters and data; permit researchers to load the output of a microarray scanning operation and to adjust the placement of each grid cell manually allow for accurate spot detection.
Allows visualization and analysis of data generated on Illumina array platforms. GenomeStudio is a data analysis tool that provides three modules: (1) Genotyping Module for the analysis of single nucleotide polymorphism (SNPs) and copy number variations (CNVs) data and detection of sample outliers, (2) Gene Expression Module for the detection of cytosine methylation at single-base resolution and identification of methylation signatures across the entire genome, and (3) Polyploid Genotyping Module for the analysis of polyploid organism genotyping data.
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.
An easy-to-use application for microarray, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), AltAnalyze will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, AltAnalyze provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichment and more).
Provides a powerful and integrated platform for the analysis of microarray gene-expression data. J-Express includes a range of analysis tools and a project management system supporting the organization and documentation of an analysis project. The software offers a choice of different unsupervised analysis methods, including clustering and projection methods. J-Express can also serve to analyze any set of objects where each measurement is represented by a multidimensional vector.
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.
A Food and Drug Administration (FDA) bioinformatics tool that has been widely adopted by the research community for genomics studies. It provides an integrated environment for microarray data management, analysis and interpretation. Most of its functionality for statistical, pathway and gene ontology analysis can also be applied independently to data generated by other molecular technologies. ArrayTrack has added capability to manage, analyse and interpret proteomics and metabolomics data after quantification of peptides and metabolites abundance, respectively. Annotation information about single nucleotide polymorphisms and quantitative trait loci has been integrated to support genetics-related studies. Other extensions have been added to manage and analyse genomics data related to bacterial food-borne pathogens. By providing powerful but easy-to-use utilities, ArrayTrack is positioned to assist in making integrated, contextualised analyses more common, which, in turn, will help to harness genetic knowledge to improve the protection of public health.