Up: Components summary Author

Marko Laakso

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.
AlleleCounter 1.2.1 genotypes frequencies, naDist Calculates genotype frequencies of a SNPMatrix.
Ant 2.0 data0, data1, data2, data3, data4, data5, data6, data7, data8, data9, array0, array1, array2, config, script output0, output1, output2, output3, output4, output5, output6, output7, output8, output9 Anduril wrapper for Apache Ant.
BiomartAnnotator 1.3 filter annotations, databases Fetches attributes with given filters using BioMart.
BoxPlot 1.3.1 in1, in2, in3, groups, dataPoints out Creates box plots for numeric data.
ClusterAnnotator 1.0 data, annotations originalPlot, annotPlot, splits Produces a hierarchical clustering of the samples and assigns the provided annotations to the brances of the clustering tree.
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.
ClusterReport 1.1 matr report, tree Performs a hierarchical clustering of samples.
CorrelationReport 1.1 matr report, correlation Creates a correlation report that shows how much columns of a numeric matrix correlate with each other.
CSV2FASTA 1.0 in out Converts the given comma separated value file to a FASTA file.
CSV2IDList 1.4 in1, in2, in3, in4, in5, in6, in7, in8, in9, array out Extracts columns from each given CSV file and prints their content out without duplicates.
CSV2Latex 2.3 tabledata, refs report Converts the given comma separated value file to a LaTeX table.
CSV2SetList 1.1 table1, table2, table3, table4, table5, table6, table7, table8, table9, tables lists Extracts identifier columns from the given CSV files and prints them out without duplicates.
CSVCleaner 2.2 in out Cleans up CSV outputs, optionally removes file headers, quotations and unused columns, and can reorder and rename columns.
CSVFilter 1.1.1 in, aux, includeColumnsFile out Filters columns and/or rows from CSV files using flexible criteria.
CSVListJoin 3.2 folder, in, in1, in2, in3, in4 out Combines the content of input files into a single CSV file.
DEGReport 1.1.1 deg, geneAnnotation, expr summary, genelist Creates a LaTeX report on differentially expressed genes (DEGs).
DESeqExpr 1.0 geneCounts, sampleNames expr, log2 Provides a gene expression matrix using DESeq.
DocumentGenerator 1.1 body1, body2, body3, body4, body5, body6, body7, bibtex, abstractText, appendix document Creates a PDF document from the given LaTeX elements and of the system configuration.
EnsemblDNA 1.0 regions, connection sequences Fetches DNA sequences from the Ensembl database.
ExclusiveCombiner 1.1 item1A, item1B, item1C, item1D, item1E, item2A, item2B, item2C, item2D, item2E, item3A, item3B, item3C, item3D, item3E itemA, itemB, itemC, itemD, itemE Binds one set of inputs to the output ports.
ExpandCollapse 1.4 in out Converts between the two possible representations of a relations with multivalued columns.
ExpressionExtremes 1.3 in out Selects differentially expressed genes using expression values as criterion.
ExprMixtureModel 1.4 expr, annot, groups stats, report, samplesets Provides a mixture model fit of two normal distributions for the given genes.
FolderCombiner 1.4 in1, in2, in3, in4, in5, in6, in7, in8, in9, in, file1, file2, file3, file4, file5, file6, file7, file8, file9, files out Copies files from input folders to output folder.
GenotypeComparator 1.7 caseF, controlF statistics Compares the allele and genotype differences between two sets of genotype frequencies.
GOClustering 1.1.3 goAnnotations, expr, similarityTable report, clusters Clusters genes based on their gene ontology (GO) annotations.
GOEnrichment 1.0.4 goAnnotations, enrichmentTable goTerms, graphBP, graphCC, graphMF Computes enriched GO terms in a set of genes or proteins.
GOFilter 1.2 bioAnnotation, in out Filters gene lists based on Gene Ontology annotations.
GOSearch 1.1 bioAnnotation, go hits Filters gene lists based on Gene Ontology annotations.
GraphAnnotator 1.1 graph, graphAttributes, vertexAttributes, edgeAttributes graph, graphAttributes, vertexAttributes, edgeAttributes Inserts or extracts attributes from GraphML files using CSV files.
GSEAAnalyzer 1.0 annotation, expr, sampleGroupTable report, ResultTable Performs Gene Set Enrichment Analysis by using category definitions from KEGG or GO.
IDDistribution 1.3 table1, table2, table3, table4, table5, table6, table7, table8, table9, array out Extracts one column from the given CSV file and prints the frequencies of its values.
KaplanMeier 2.2 survival, annotation report, statistics, plots Produces a Kaplan-Meier plot representing survival estimates based on the given data.
KorvasieniAnnotator 1.9 sourceKeys, connection bioAnnotation Converts gene, transcription, and translation identifiers using Korvasieni.
LatexAttachment 1.0 file1, file2, file3, file4, file5, file6, file7, file8, file9 report Constructs a LaTeX fragment that includes attachments for the given files.
LatexCombiner 1.5 latex1, latex2, latex3, latex4, latex5, latex6, latex7, latex8, latex9, array, resources document Combines several LaTeX fragments into one LaTeX document.
LatexTemplate 1.4.2 docAbstract, bibtex, bibtex1, bibtex2, bibtex3, bibtex4, bibtex5 header, footer Creates LaTeX header and footer files that are inserted to the beginning and the end of the LaTeX report.
LiftOver 1.1 regions, chain out Converts chromosome region coordinates from one genome build to another.
Logo 1.6 motifs, annot, subset report Generates sequence logos for the given DNA motifs.
MarkerCorrelations 1.1 genotypes markerGroups, keyMarkers Combines correlating markers from the SNPMatrices.
MEMERunner 1.2 sequences motifs, annot, report Finds enriched motifs from the given set of DNA sequences.
MotifMatch 1.7.1 motifs, sequence, seqSelection, bgIn, exclude hits, frequencies, bgOut Aligns the given motifs against the DNA sequencies.
NextGene 1.5.1 sourceKeys, connection bioAnnotation Finds the closest gene, exon, or transcript for the given loci.
PairCorrelation 1.1 data, pairs stats, skipped Calculates correlations for the row pairs.
PCAxisReader 1.0 in out Converts a PC-Axis file to a CSV.
PeakScore 1.2 in out Calculates a cumulative score for each gene having some regions assigned to it.
PINA 1.1 query interactions, network Finds the interacting proteins of query proteins for a list of query Uniprot ACs.
Plot2D 1.0 y, x, labels, plotAnnotator out Creates scatter, line or bar plots where Y and X coordinates come from CSV files.
Properties2Latex 1.2 props1, props2, props3, props4, props5, props6, props7, props8, props9 report Converts a set of properties files into a LaTeX fragment.
QueryReport 1.2 query, table1, table2, table3, table4, table5, table6, table7, table8, refs report, data Executes an SQL query and prints it with the result table.
RConfigurationReport 1.0 packageList report, citations Generates a report about the versions and the purposes of the selected R packages.
RefSNPAnnotator 1.1.3 rsIDs annotations, geneChanges, databases Fetches annotations for given SNP rsID's with biomaRt.
RegionOverlap 1.2 regions1, regions2 regions Produces a list of overlapping DNA regions.
RegionReport 1.1 regions, chromosomes report Generates statistics about the DNA regions.
REvaluate 2.2 script, table1, table2, table3, table4, table5, var1, var2, var3, inArray table, outArray, optOut1, optOut2, optOut3, document Executes an R script that generates a matrix from the given data.
RiskRatioPlot 1.0 in out Creates a visualization for a list of risk ratios and their confidence intervals.
RowCount 1.1 relation dimensions, category Classifies the number of rows of an input CSV to be either small, medium, or large.
SampleExpression 1.1 expr, groups indicator, logratio, deviation Creates a -1/0/1 matrix that indicates whether a given gene/probe is differentially expressed in individual samples.
SearchReplace 1.1 in, rules out Transforms the given file by replacing certain string with new values.
SegmentPlot 1.5 chrSegments plot, SignRegion Plots segmented chromosomal data.
SequenceFilter 1.0 sequences selection Filters out nucleotide sequences that do not satisfy the criteria.
SNPHelistinReader 1.2 sampleNames, markerNames, config genotypes Imports genotype data from a SNPHelistin database.
SNPKaplanMeier 1.6.1 genotypes, survival, annotations statistics, report Calculates Kaplan-Meier estimates for genotype specific survival effects.
SourceCode2Latex 1.0 in out Converts the given source code to a LaTeX fragment containing the given listing (lstset).
SQLSelect 1.1 query, queryParams, connection table Executes an SQL query and returns its results as a CSV file.
StandardProcess 1.3 input, env, arg1, arg2, arg3, arg4, arg5, arg6, arg7, arg8, arg9 stdout, stderr, optOut1, optOut2, optOut3 Executes a given system command.
TableQuery 1.3 table1, table2, table3, table4, table5, table6, table7, table8, table9, table10, table11, table12, table13, table14, table15, tables, queryFile, columnTypes table Executes an SQL query on CSV tables and creates a result table.
VertexJoin 1.4 in out, joins Simplifies the given graph by merging vertices with an equal set of edges.
WekaClassifier 1.1 data, testdata, classifydata, inClassifier outClassifier, report, confusion, evaluation, predictedClasses Creates a classifier based on the given sample data.

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