Gene expression clustering software tools | Transcription data analysis
Microarray technology has been widely applied in biological and clinical studies for simultaneous monitoring of gene expression in thousands of genes. Gene clustering analysis is found useful for discovering groups of correlated genes potentially co-regulated or associated to the disease or conditions under investigation.
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.
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.
Allows users to build large attractor networks from static gene-expression data. Hclust uses Hopfield networks for clustering, feature selection and network inference and did not require the data relative to pathway or kinetic information. The application is able to generate plots depicting the weight matrix of the network, the relaxation of the state matrix and the energy landscape.
Assess the uncertainty in hierarchical cluster analysis. Pvclust is designed for general hierarchical clustering problems. It permits users to easily obtain bootstrap-based p-values for their own dataset and preferred clustering method. The tool provides AU (approximately unbiased) p-value as well as BP (bootstrap probability) value for each cluster in a dendrogram.
A widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses. In response to the rapid increase in the amount of sequencing data produced by the next-generation sequencing technologies, a new CD-HIT program accelerated with a novel parallelization strategy and some other techniques has been developed to allow efficient clustering of such datasets.
Supports visual data exploration. GENE-E is a matrix visualization and analysis platform that includes heat map, clustering, filtering, charting, marker selection, and many other tools. In addition to supporting generic matrices, it also contains tools that are designed specifically for genomics data. GENE-E is no longer supported, but can still be downloaded. It is now recommended to use new web-based tool, Morpheus.