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InCroMAP / Integrated analysis of Cross-platform MicroArray and Pathway data

A tool for the analysis and visualization of high-level microarray data from individual or multiple different platforms. Currently, InCroMAP supports mRNA, microRNA, DNA methylation and protein modification datasets. Several methods are offered that allow for an integrated analysis of data from those platforms. The available features of InCroMAP range from visualization of DNA methylation data over annotation of microRNA targets and integrated gene set enrichment analysis to a joint visualization of data from all platforms in the context of metabolic or signalling pathways.

AgiMicroRna

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.

targetscan.Hs.eg.db

Predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA. Sites with mismatches in the seed region that are compensated by conserved 3' pairing are also identified. In mammals, predictions are ranked based on the predicted efficacy of targeting as calculated using the context scores of the sites. targetscan.Hs.eg.db provides detailed information about the latest version of the TargetScan miRNA target prediction database. This package is updated biannually.