Up: Components summary
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. |