| 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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Marko Laakso