Up: Components summary Author

Viljami Aittomaki

Component Version Inputs Outputs Description
BiomartAnnotator 1.3 filter annotations, databases Fetches attributes with given filters using BioMart.
BreakpointVisualizer 0.1.1 cna, rearrangements report Visualizes genomic breakpoints resulting from copy-number aberrations (amplifications and deletions) and chromosomal rearrangements (translocations and inversions).
HTMLTable 0.7 in, style out Creates an interactive HTML table of input data.
JASPARMotif 2.0.3 IDs motifs, annotations Writes JASPAR motif matrices into a MotifSet directory.
LimmaNormalizer 0.6 green, greenBG, red, redBG, groups logratio Normalizes two-channel and single-channel microarrays using the Bioconductor Limma package.
MDSPlot 2.2 expr, groups mdsCoOrdinates, report Plots multidimensional scaling of numeric data.
RefSNPAnnotator 1.1.3 rsIDs annotations, geneChanges, databases Fetches annotations for given SNP rsID's with biomaRt.
SigPathway 1.0 expr, samplegroup pathways Performs pathway analysis by computing NEk and NTk statistics described in Tian et al (2005).
SPIA 1.1 deg, reference pathways, pathwayGenes Performs pathway analysis using Signaling Pathway Impact Analysis (formerly known as Pathway-Express).
WekaClusterer 1.0 in out Clusters data using clustering methods implemented in Weka.
WekaTransform 1.3 in out Transforms data using filter classes implemented in Weka.

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