Data visualization software tools | Gene expression microarray data analysis
Comprehensive analysis of genome-wide molecular data challenges bioinformatics methodology in terms of intuitive visualization with single-sample resolution, biomarker selection, functional information mining and highly granular stratification of sample classes.
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.
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.
Allows visualization of microarray data. TreeView is an open source, cross-platform which offers several views, including dendrogram, scatterplot, karyoscope and alignment, with visual cues to show which genes are selected. The software provides fine control over the appearance of dendrogram.
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.
Visualizes correlation matrix. The corrplot package is a graphical display of a correlation matrix, confidence interval. It also contains some algorithms to do matrix reordering. It offers some functions as a reorganization of a correlation matrix. The details are paid great attention to. It can also visualize a general matrix by setting is.corr = FALSE, rectangle(s) drawing around the chart of correlation matrix and many others.
Constructs images from matrices. Matrix2png can be used to build images on the fly for display in web applications. It provides functions for the controls of value-to-color mapping. It offers a range of preset color schemes and includes some suitable for color-blind viewers. This tool allows users to control image size, contrast, outlier trimming, the displayed data range, the display of text row and column labels, and, importantly, a scale bar.
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.