Enables visualization and statistical analysis of microarray gene expression, copy number, methylation and RNA-Seq data. BRB-ArrayTools provides scientists with software to (1) use valid and powerful methods appropriate for their experimental objectives without requiring them to learn a programming language, (2) encapsulate into software experience of professional statisticians who read and critically evaluate the extensive published literature of new analytic and computational methods, and (3) facilitate education of scientists in statistical methods for analysis of DNA microarray data.
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.
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.
Provides the premier enterprise solution for data content, framework and graphical user interface for omic and next-generation sequencing data analysis. Array Suite (Array Studio and Array Server) differs from standard desktop solutions or open source solutions, with Array Studio providing the graphical user interface for NGS and omic analysis and visualization and Array Server providing the enterprise back-end solution for project management, sample management and data storage.