Up: Components summary Author

Sirkku Karinen

Component Version Inputs Outputs Description
CircosPlot 0.7 data, data2, data3, data4, data5, data6, data7, data8, data9, data10, data11, dataAnnotation, plotAnnotation, links, highlights, plotParams, karyotype circos, ideogram, ticks, plot Draws circos plots from genomic data.
ClusterPlotCombiner 1.0 y, x, ySummary, xSummary, originalData, labels, plotAnnotator out Creates scatter, line or bar plots where Y and X coordinates come from CSV files.
CSVSplitColumns 0.1 in out Splits CSV into new files according to columns.
Excel2Text 0.1 in out Converts an Excel 97 xls-sheet to a text file.
ExpressionImport 0.1 datasets, sampleNames expr Reads expression data, applies all available normalization methods and returns a record with normalized datasets.
ExtensiveCSVJoin 0.1 files, fileDefs join Combines and cleans many files.
FillNA 0.1 in out Fills NA values with linear interpolation or previous value.
GetReads 1.0 alignment, array reads Visualizes reads that are aligned to a given position.
HTMLCombiner 0.1 head, body, script, style, headArray, bodyArray, scriptArray, styleArray, subFolder out Combines a HTML page from parts.
HTMLExtractor 0.1 html1, html2, htmlArray head, body, script, style Extracts HTML parts from a site.
InteractionPlot 1.0 interactions, expression, groups plot Plots the distribution of the expression of two genes.
Labels2Columns 1.1 in out Reads columns of data, the unique entries of the label column are transposed as column names.
LocationVariation 1.0 locations, variationDatabase variations, populations Gets variation from Ensembl from a genomic location.
Plink 1.1 pedFile, mapFile, file1, file2, file3 result1, result2, result3, result4, result5 Wraps Plink software that allows various genome wide SNP data manipulations and analyzes.
Plot2D 1.0 y, x, labels, plotAnnotator out Creates scatter, line or bar plots where Y and X coordinates come from CSV files.
RangeMatch 1.0 positions, ranges result Component for 'left join' using keys and ranges.
SNPs3DSearch 1.0 queryFeatures associatedGenes Fetches disease associated genes from the SNPs3D database.
Summarization 1.0 data summarization Summarizes information from region using sliding window or group ids (same as SQL GROUP BY).
When sliding window is used, input file needs to be sorted according to locationCol Variation.jar is in microarray bundle.
VariantFilter 1.0 in, annotationArray, annotation out, alleleCount Filters variants based on allele frequencies in the data.
VCF2CSV 1.0 vcf annotations, samples Converts variation calls in VCF format to CSV.
WekaAPriori 1.1 in, selectedColumns out Mines association rules using a priori algorithm: R.
WekaAttributeSelection 1.0 in out Selects parameters using Weka AttributeSelection classes.
WekaClassifier 1.1 data, testdata, classifydata, inClassifier outClassifier, report, confusion, evaluation, predictedClasses Creates a classifier based on the given sample data.
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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