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Data Import

Description Data import from platforms such as microarrays.
Child categories
Affy AffyReader SNPArrayReader AffyNormalization AffySNPFetch
Agilent ACGHsegment AgilentReader
Illumina SNPArrayReader
Component Version Inputs Outputs Description
AffyNormalization 1.0 affy, sampleNames report Reads in Affymetrix gene expression microarrays and compares various normalization methods.
AffyReader 1.1.2 affy, sampleNames expr, exprRaw, groups Imports gene expression or exon array data from Affymetrix CEL-files.
AgilentImport 1.0 agilentInput, sampleNames, groups logratio, channels, probeAnnotation, sampleAnnotation, groups, qcReport Imports Agilent microarray data, merges duplicate probes and creates a log ratio matrix.
AgilentReader 1.0.1 agilent, sampleNames green, green2, red, red2, probeAnnotation, sampleAnnotation, groups Imports data from microarray text files such as Agilent CSV files.
AnnotateDrugs 1.0 in, annotations out Annotate drug concentrations.
ExpressionImport 0.1 datasets, sampleNames expr Reads expression data, applies all available normalization methods and returns a record with normalized datasets.
IlluminaReader 1.1.1 illumina, sampleNames expr, probeAnnotation, groups Imports gene expression data from Illumina BeadStudio output files.
LimmaNormalizer 0.6 green, greenBG, red, redBG, groups logratio Normalizes two-channel and single-channel microarrays using the Bioconductor Limma package.
MicroarrayReader 0.7 data, sampleNames channel1, channel2, sampleAnnotation Reads in expression microarray data produced by feature extraction software.
MicroplateReader 1.0 in, annotations out Reads multiple XLSX files generated by a fluorescence/luminescence reader for a 96 or 384 well plate and converts it into a tab-delimitted CSV file with the correct annotations for each well.
PCAxisReader 1.0 in out Converts a PC-Axis file to a CSV.
SNPArrayReader 1.7 dataDir, sampleNames genotypeMatrix, markerNames, copynumberMatrix, probeAnnotation Imports genotype data from Illumina SNP and Affymetrix SNP 6.0 or 5.0 files.
SNPHelistinReader 1.2 sampleNames, markerNames, config genotypes Imports genotype data from a SNPHelistin database.
SQLSelect 1.1 query, queryParams, connection table Executes an SQL query and returns its results as a CSV file.

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