MicroRNA microarray technology is a powerful high-throughput tool capable of monitoring the expression of thousands of microRNAs at once within tens of samples processed in parallel in a single experiment. While many of the same tools for analyzing mRNA expression arrays can be applied to the analysis of miRNA data, there are distinct differences between the two platforms which necessitate special use of some methods.
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.
A package for the pre-processing and differential expression analysis of Agilent microRNA array data. For the pre-processing of the microRNA signal, AgiMicroRNA incorporates the robust multiarray average algorithm, a method that produces a summary measure of the microRNA expression using a linear model that takes into account the probe affinity effect. To obtain a normalized microRNA signal useful for the statistical analysis, AgiMicroRna offers the possibility of employing either the processed signal estimated by the robust multiarray average algorithm or the processed signal produced by the Agilent image analysis software. It also incorporates different graphical utilities to assess the quality of the data. AgiMicroRna uses the linear model features implemented in the limma package to assess the differential expression between different experimental conditions and provides links to the miRBase for those microRNAs that have been declared as significant in the statistical analysis.
Assists users in investigating normalized omics large datasets. Qlucore Omics Explorer is a modular platform divided into four main functionalities (i) Visualization includes features for generating various plots types including principal component analysis (PCA) plots and real-time visualization; (ii) Exploration furnishes tools for comparing, browsing and selecting targeted information (iii) Analysis includes statistical methods such as quadratic regression, f-tests, or ANOVA and (iv) Sharing allows users to export results as multiple formats including videos or variable lists.
Takes the MiChip miRNA microarray .grp scanner output files and parses these out, providing summary and plotting functions to analyse MiChip hybridizations. A set of hybridizations is packaged into an ExpressionSet allowing it to be used by other BioConductor packages.
Permits normalization of microarray data for removing bias and noise variability. LoessM is a normalization procedure, based on the loess algorithm, that scales expression data on the global median expression rather than on zero, as usually done for whole-genome arrays. Combined with eCADS, a biological replicates dye-swap design, the software is able to maintain the correct structure of expression data.
Analyses large-scale expression datasets. It utilizes curated sets of 3’ UTRs to attach sequences to these genes and then applies the Sylamer algorithm for detection of miRNA or siRNA signatures in those sequences. SylArray allows researchers from a broad area of expertise to perform fast and accurate detection of small RNA signatures in their gene-expression datasets.
Allows analysis of Exiqon miRCURY LNA™ microRNA Array data. miRCURY LNA microRNA Array Analysis Software contains ImaGene® 9, Nexus Expression™ 3 from BioDiscovery and settings files for analysis. The two programs help to convert tiff images of the scanned slides into useful information. The software allows to identify differentially expressed microRNAs and analyzes expression patterns across samples.