See also: Data type documentation    Category summary

Table of contents

Component summary

Name Version Inputs Outputs Description
ACGHnorm 1.4 casechannel, control, admixtureMatrix, probeAnnotation casechannel, controlchannel, fit Normalizes two channel array CGH data with LOESS, median or mode.
ACGHsegment 2.0 caseChan, geneAnnotation report, segments, tholds, lossProbs, gainProbs, normProbs, rawSegments, frequency Segments Array CGH data with the Circular Binary Segmentation (CBS) algorithm and produces hard or soft copy number aberration calls.
ActivityStatus 1.0.2 measures status Converts numerical measures to gene activity indicators.
AffyReader 1.1.2 affy, sampleNames expr, exprRaw, groups Imports gene expression or exon array data from Affymetrix CEL-files.
AgilentReader 1.0.1 agilent, sampleNames green, green2, red, red2, probeAnnotation, sampleAnnotation, groups Imports data from microarray text files such as Agilent CSV files.
AlleleCounter 1.2.1 genotypes frequencies, naDist Calculates genotype frequencies of a SNPMatrix.
AndurilEvaluate 1.1 script, inputs outputs, execution, log, script Run an Anduril network as a component.
Ant 2.0 data0, ..., data9, array0, array1, config, script output0, ..., output9 Anduril wrapper for Apache Ant.
Array2CSV 1.0 array csv Reads an array, and returns a CSV with File column converted to absolute paths.
Array2Folder 1.1 array, template folder Transforms an array into a physical folder.
ArrayCombiner 1.1 array1, ..., array20 array Combines multiple arrays into one using set operations on array keys.
ArrayConstructor 1.0 file1, ..., file99 array Constructs an array from atomic elements.
ArrayExtractor 1.0 array file1, ..., file9 Extracts elements from an array.
ArraySplitter 1.1 array array1, ..., array9 Divides array keys evenly in to N arrays.
ArrayTransformer 1.0 original, auxiliary outputArray Transform arrays by removing elements, renaming keys or sorting the elements.
AttributeVisualizer 1.0.1 annotation, matrix report Visualizes multidimensional attributes using a heat map together with a clustering dendrogram.
BashEvaluate 1.4.2 array1, array2, array3, script, var1, ..., var6, vararray script, stdOut, stdErr, optOut1, optOut2, optOut3, folder1, folder2, array1, array2 Executes a Bash script that generates any output from the given data or other inputs.
BiomartAnnotator 1.3 filter annotations, databases Fetches attributes with given filters using BioMart.
BoxPlot 1.3.1 matr1, matr2, matr3, groups, dataPoints report Creates box plots for numeric data.
CandidatePathway 1.4 hits, linkStyles, within graph, legend Generates a mixed pathway that contains the given bioentities and the biological links between them.
CellLineQuery 1.0 sample, geneIDs, cellNames similarCells, DrugSens, QueryResults Performs one of two tasks defined by task parameter.
CircosPlot 0.7 data, data2, ..., data11, dataAnnotation, plotAnnotation, links, highlights, plotParams, karyotype circos, ideogram, ticks, plot Draws circos plots from genomic data.
ClusterReport 1.1 matr report, tree Performs a hierarchical clustering of samples.
CN2GECollection 1.0 exprMatrix, cnaMatrix, exprAnnotation, exprRefMatrix, cnaRefMatrix, labels concomitantGenes, concomitantGenes2, plot Encapsulates three algorithms with similar inputs for copy number to RNA expression integration.
CNACaller 1.0 segments, probeAnnotation regions Calls significant copy number alterations from a group of segmented copy number alteration profiles.
CNGEIntegrator 1.1.0 CNAProbLoss, CNAProbGain, CNAProbNorm, exprMatrix, exprAnnotation integrationResult Performs one of two possible nonparametric tests for the detection of copy number induced differential gene expression.
CompareImage 0.3 expected, image Compare images.
ConfigurationReport 1.0 compStyles report, topology, currentStyles Creates a LaTeX report for component network topology and configuration.
ConfigurationStatistics 1.0 children Calculates workflow statistics about the associations between the component types.
CorrelationReport 1.1 matr report, correlation Creates a correlation report that shows how much columns of a numeric matrix correlate with each other.
CSV2Array 1.1 csv array Reads a CSV, and returns an array based on selected columns.
CSV2Excel 1.3 csv, csv2, ..., csv9, array, style, refs excelFile Converts a file from CSV format to Excel 97 format.
CSV2FASTA 1.0 csv fasta Converts the given comma separated value file to a FASTA file.
CSV2GraphML 1.0 matrix graph Converts a matrix or CSV representation of a graph to GraphML.
CSV2IDList 1.4 table1, ..., table9, array ids Extracts columns from each given CSV file and prints their content out without duplicates.
CSV2JSON 1.0 csv json Transforms a CSV file to JSON format.
CSV2Latex 2.3 tabledata, refs report Converts the given comma separated value file to a LaTeX table.
CSV2SetList 1.1 table1, ..., table9, tables lists Extracts identifier columns from the given CSV files and prints them out without duplicates.
CSVCleaner 2.2 original table Cleans up CSV outputs, optionally removes file headers, quotations and unused columns, and can reorder and rename columns.
CSVFilter 1.1.1 csv, auxiliary, includeColumns csv Filters columns and/or rows from CSV files using flexible criteria.
CSVJoin 1.1 csv1, ..., csv8, csvDir, array csv Joins rows from two or more CSV files from all the inputs, optionally using one column as a matching key.
CSVListJoin 3.1 folder, files, file1, ..., file9 join Combines the content of input files into a single CSV file.
CSVSort 1.2 csv, array csv Sorts and merges CSV files.
CSVSplit 1.0 csv array Divides the content of the given CSV to an array of multiple CSV files.
CSVSummary 1.0 csv summary Summarises values for rows of a file according to a column label or the whole file to single row.
CSVTransformer 1.1 csv1, columnNames, array transformed Transforms CSV files using R expressions.
DEE2DEG 1.0 dee, dbConnect deg Find differentially expressed genes (DEG) based on differentially expressed exons (DEE).
DEGReport 1.1.1 deg, geneAnnotation, expr summary, genelist Creates a LaTeX report on differentially expressed genes (DEGs).
Directed2Undirected 1.0 graph graph Converts a directed graph into undirected graph.
DrugPathway 1.4 targets, drugs, linkStyles, status graph, legend, status Produces a pathway model of possible drugs targeting some of the given genes.
DuplicateQuality 1.0 expr, geneAnnotation report Estimates microarray chip quality by printing expression distributions for duplicate probes.
EnsemblDNA 1.0 regions, connection sequences Fetches DNA sequences from the Ensembl database.
EntrezAnnotator 1.0 query annotation Retrieves database records from NCBI Entrez, including gene annotation, PubMed references and sequences.
Excel2CSV 0.1 excelFile csv Converts an Excel 97 xls-sheet to a CSV file.
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.
ExonAnnotator 1.0 query, dbConnect table Maps gene, transcript or exon Ensembl IDs to one another via the Ensembl query interface.
ExonExpression 1.0 expr, sample, exon ExonExpr Converts exon expression matrix for a list of exons of interest.
ExonToPeptide 1.0 ExonList, connection ExonSeq, PeptideSeq Fetches exon-peptide sequences of query exon list.
ExpandCollapse 1.4 relation relation Converts between the two possible representations of a relations with multivalued columns.
ExperimentSetup 1.2 groups, idlist report, graph Creates a report that displays all sample groups using a table and a graph that visualizes the sample groups and their relations.
ExpExpIntegration 1.1 labelMatrix, exprMatrix Values Integrates gene/transcript/other expression data with binary explanatory data derived in some way.
ExpressionExtremes 1.3 expr deg Selects differentially expressed genes using expression values as criterion.
ExpressionGraph 1.6 graph, status, linkTypes graph Simplifies the given graph by removing absent genes and vertices that are in contradiction to the given expression profile.
ExprMethylCGH 1.1.1 exprMatrix, cghMatrix, methylMatrix statistics Integrates expression data with methylation and CGH data by using two label matrices of ones and zeros.
ExprMixtureModel 1.4 expr, annot, groups stats, report, samplesets Provides a mixture model fit of two normal distributions for the given genes.
FoldChange 1.1 logratio deg Selects differentially expressed genes using fold change as criterion.
Folder2Array 1.2 folder1, ..., folder9 array Constructs an array from folder contents.
FolderCombiner 1.4 folder1, ..., folder9, folders, file1, ..., file9, files folder Copies files from input folders to output folder.
FolderExtractor 1.0 folder file1, ..., file9 Extracts files from a folder.
FolderSplitter 1.1 dir dir1, ..., dir9 Divides files evenly from a folder in to N folders.
GeneCount 1.0 expr1, ..., expr8, geneAnnotation report Produces a LaTeX report that shows the number of genes or features under analysis in various phases of an Anduril script.
GeneInfo 1.0 expr1, expr2, expr3, geneAnnotation, groups report Prints detailed information on single genes.
GeneTable 1.1.1 idlist, expr, geneAnnotation, groups, sampleAnnotation csvfiles Compiles gene ID sets into CSV files that contain gene annotations and expression.
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, idlist idlist Filters gene lists based on Gene Ontology annotations.
GOProbabilityTable 1.0 goAnnotation similarityTable, enrichmentTable Creates custom a priori probability tables for GO similarity and enrichment analysis.
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.
GraphMetrics 1.0 graph graphMetrics, vertexMetrics Computes various graph metrics for a GraphML file.
GraphSplitter 1.0 graph array Splits a graph into subgraphs that are either connected or strongly connected (case of directed graph) components.
GraphVisualizer 1.2 graph figure Creates a visualization of a graph using Graphviz.
GSEAAnalyzer 1.0 annotation, expr, sampleGroupTable report, ResultTable Performs Gene Set Enrichment Analysis by using category definitions from KEGG or GO.
GSVDIntegrator 1.0.1 exprMatrix, cnaMatrix, exprAnnotation integrationResults, cghResults, annotations Extracts variation patterns from two matrices based on the generalized singular value decomposition.
HeatMapReport 2.2 matr, rowLabels, colLabels report, array Clusters samples hierarchically and draws the corresponding dendrograms and heat map.
HTMLReport 1.0 table1, ..., table5, mapping, matrix1, matrix2, matrix3, matrixMapping, images, imageMapping, refs, labels report Visualizes CSV files and their relationships using statically generated HTML files.
HTMLTable 0.7 data, style table Creates an interactive HTML table of input data.
IDConvert 1.0 csv, conversionTable csv Converts IDs from a column in a CSV file to other type of IDs and/or combines duplicated rows into one.
IDDistribution 1.3 table1, ..., table9, array ids Extracts one column from the given CSV file and prints the frequencies of its values.
IlluminaAnnotator 13.10 csv bioAnnotation Fetches genomic annotations for Illumina methylation and expression array probes.
IlluminaNormalization 1.0 exprRaw exprNorm Performs between array normalization for an input matrix.
IlluminaPlot 1.1 expr plot Produces quality control plots.
IlluminaReader 1.1.1 illumina, sampleNames expr, probeAnnotation, groups Imports gene expression data from Illumina BeadStudio output files.
INPUT   in Imports an external input file or directory to the pipeline.
JASPARMotif 2.0.3 IDs motifs, annotations Writes JASPAR motif matrices into a MotifSet directory.
JCSVJoin 1.0 csv1, ..., csv8, csvDir, array csv Java implementation of R CSVJoin component.
KaplanMeier 2.2 survival, annotation report, statistics, plots Produces a Kaplan-Meier plot representing survival estimates based on the given data.
KeywordMatcher 1.0 annotation, query mapping Identifies gene/protein IDs using fuzzy keyword matching between gene aliases and descriptions.
KGML2GraphML 1.0 kgml pathway Converts a KEGG pathway (KGML) to a GraphML file.
KorvasieniAnnotator 1.8.2 sourceKeys, connection bioAnnotation Converts gene, transcription, and translation identifiers using Korvasieni.
Labels2Columns 1.1 csv csv Reads columns of data, the unique entries of the label column are transposed as column names.
LatexAttachment 1.0 file1, ..., file9 report Constructs a LaTeX fragment that includes attachments for the given files.
LatexCombiner 1.5 latex1, ..., latex9, array, resources document Combines several LaTeX fragments into one LaTeX document.
LatexPDF 1.1 document, header, footer document, completeDocument Compiles a LaTeX document into Portable Document Format (PDF).
LatexTemplate 1.4.2 abstract, bibtex, bibtex1, ..., 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 regions Converts chromosome region coordinates from one genome build to another.
LimmaNormalizer 0.6 green, greenBG, red, redBG, groups logratio Normalizes two-channel and single-channel microarrays using the Bioconductor Limma package.
LimmaStat 1.0 expr, sampleAnnotation sigTarget Select differentially expressed probesets, exons or transcripts from probeset, exon or transcript expression data by using limma statistical test.
LinearBinner 1.0 csv binned, cluster A very basic clustering-like method.
LinearNormalizer 1.0 matrix matrix Normalizes the input matrix column-wise.
LocationVariation 1.0 locations, variationDatabase variations, populations Gets variation from Ensembl from a genomic location.
MACS 1.1 treatment, control peaks, negativePeaks, report, wiggle, bedGraph Finds peaks from aligned short-reads.
MarkerCorrelations 1.1 genotypes markerGroups, keyMarkers Combines correlating markers from the SNPMatrices.
MatlabEvaluate 1.0 script, table1, ..., table5, var1, var2, ..., var9 table, optOut1, optOut2, optOut3, document Executes a Matlab script that generates a matrix from the given data.
MatrixRank 1.0 matrix ranks Computes ranks of values in a matrix.
MatrixTranspose 1.0 matrix matrix Transposes a matrix.
MDSPlot 2.2 expr, groups mdsCoOrdinates, report Plots multidimensional scaling of numeric data.
MeapNormalization 2.0 affy, sampleNames normalized Prepares normalized data at probe level.
MeapQuantification 2.0 normalized, dbConnect ExonExpr, SpliceVariantExpr, GeneExpr Quantify expression data on exon, splicing variant or gene level.
MeapVisualizer 1.0 expr, geneList, dbConnect, sample report Generate visualization for genes of interest with spliced isoforms.
MEMERunner 1.2 sequences motifs, annot, report Finds enriched motifs from the given set of DNA sequences.
ModelicaCompiler 0.5 sourceModel binaryModel, flatModel Compile a Modelica model into binary form using OpenModelica.
ModelicaSimulator 0.5 binaryModel, parameters timepoints Simulate a Modelica model by executing a compiled model.
MoksiskaanConnector 1.1 connection, report Needs to be called once in order to gain access to Moksiskaan database.
MotifMatch 1.7.1 motifs, sequence, seqSelection, bgIn, exclude hits, frequencies, bgOut Aligns the given motifs against the DNA sequencies.
NextBioentity 1.0 sourceKeys, connection bioAnnotation Finds the closest bioentity for the given loci.
NextGene 1.5.1 sourceKeys, connection bioAnnotation Finds the closest gene, exon, or transcript for the given loci.
OUTPUT   out out Exports a result file or directory to an output directory.
PAGE 1.0 annotation, expr, statistic, sampleGroupTable report, ResultTable Performs parametric analysis of gene set enrichment (PAGE) by using category definitions from KEGG, GO or any other wanted categorization.
PairCorrelation 1.1 data, pairs stats, skipped Calculates correlations for the row pairs.
Pathway2Cytoscape 1.2.1 pathway, groups session Prepares Moksiskaan pathways to Cytoscape sessions.
Pause   Halts pipeline execution.
PCA 1.0 matrix loadings, scores, variation PCA performs a principal component analysis on a given data matrix based on singular value decomposition (SVD).
PeakScore 1.2 genes scores Calculates a cumulative score for each gene having some regions assigned to it.
PiispanhiippaAnnotator 1.2 sourceKeys, connection bioAnnotation, query A bioentity querying interface for Moksiskaan.
PINA 1.1 query interactions, network Finds the interacting proteins of query proteins for a list of query Uniprot ACs.
PipelineInput 1.1 name, n Read a previous Anduril pipeline execution folder as an input.
Plot2D 1.0 y, x, labels, plotAnnotator plot Creates scatter, line or bar plots where Y and X coordinates come from CSV files.
PlotHTML 0.1 data, template plot Creates scatter, line or bar plots where Y and X coordinates come from JSON files.
PlotTreeHTML 1.0 treeStructure, metadata, imageData plot Produces a plot of a tree (or forest) in a html page.
PointDistance 1.1 points, data csv Measures the nearest data point (data) distance for each reference point (point).
Properties2Latex 1.2 props1, ..., props9 report Converts a set of properties files into a LaTeX fragment.
PythonEvaluate 0.5 script, table1, ..., table5, var1, var2, array, folder, vararray table, array, optOut1, optOut2, optOut3 Executes an Python script.
QuantileFilter 1.0 matrix, matrix2 matrix, matrix2 Filters values from numeric matrices that are below or above quantile limits.
Randomizer 1.0 matrix Generates numeric matrices filled with random values.
RandomSampler 0.5 input sample Randomly selects rows and columns from a text or CSV file without replacement.
RangeMatch 1.0 positions, ranges result Component for 'left join' using keys and ranges.
RankScore 1.0 classes, ranks, genes scores, classes Calculates a score matrix for a dichotomially classified set of samples.
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.
RegionReport 1.1 regions, chromosomes report Generates statistics about the DNA regions.
REvaluate 2.2 script, table1, ..., table5, var1, var2, array table, array, optOut1, optOut2, optOut3, document Executes an R script that generates a matrix from the given data.
RiskRatioPlot 1.0 data report Creates a visualization for a list of risk ratios and their confidence intervals.
RNAFold 1.0 sequence structure Predicts RNA secondary structure using Vienna RNA Package energy minimization function.
RowCount 1.1 relation dimensions Classifies the number of rows of an input CSV to be either small, medium, or large.
Rsync 1.0 file, folder file, folder Uses rsync to fetch or push files.
SampleCombiner 1.0 expr, groups expr Combines expression data from several samples into one by taking means, medians or log ratios.
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.
SampleGroupCreator 1.2.2 data1, data2, data3 groups Creates sample group tables based on sample names read from data files.
SaveBioentities 1.1 bioentities Stores the given bioentities into the database.
SaveGORegulations 1.1 bioAnnotation, go Stores positive and negative regulations of the GO terms to the database.
SaveStudy 2.2 hits report Saves results of an individual study into the database.
SaveXrefs 1.0 bioentities Adds external references for the given bioentities.
SBML2GraphML 1.0 model graph Visualizes an SBML model as a GraphML file.
SBML2HTML 1.0 model report Prints the contents of an SBML model as a HTML file.
SBMLSimulator 1.2 model plot, timepoints Simulates an SBML model using SBML ODE Solver.
SBMLTable 1.3 model, species, reactions, parameters, compartments, rules, events, annotations model, species, reactions, parameters, compartments, rules, events, annotations Extracts SBML attributes into a CSV file, or imports attributes from a CSV file.
ScalaEvaluate 0.1 script, table1, ..., table5, var1, var2 table, optOut1, optOut2, optOut3 Executes a Scala script.
ScoreMatrix 1.4 scores Generates a matrix of bioentity rows and study columns where each cell represents the score of the corresponding hit.
SearchReplace 1.1 file, rules file 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.
SetTransformer 0.6 transformation, set1, ..., set5 result Transforms sets using union, intersection, difference and other functions.
SigPathway 1.0 expr, samplegroup pathways Performs pathway analysis by computing NEk and NTk statistics described in Tian et al (2005).
SimpleWebPage 1.2 folder, array, content, style, annotation html Creates a simple web page, for publishing a list of files.
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.
SNPKaplanMeier 1.6.1 genotypes, survival, annotations statistics, report Calculates Kaplan-Meier estimates for genotype specific survival effects.
SNPs3DSearch 1.0 queryFeatures associatedGenes Fetches disease associated genes from the SNPs3D database.
SourceCode2Latex 1.0 source report Converts the given source code to a LaTeX fragment containing the given listing (lstset).
SpatialContrast 1.0 expr, geneAnnotation report Finds two spatial regions in expression data that have a maximum contrast in average expression value.
SpatialPlot 1.4 geneAnnotation, channel1, logratio report Creates spatial plots for red/green channels, log ratios and spot quality.
SPIA 1.1 deg, reference pathways, pathwayGenes Performs pathway analysis using Signaling Pathway Impact Analysis (formerly known as Pathway-Express).
SQLSelect 1.1 query, queryParams, connection table Executes an SQL query and returns its results as a CSV file.
StandardProcess 1.2 input, env, arg1, ..., arg9 stdout, stderr, optOut1, optOut2, optOut3 Executes a given system command.
StatisticalTest 1.1 matrix, matrix2, groups pvalues, idlist Computes p-values using statistical tests, optionally with correction for multiple hypotheses.
StringInput   in Turns a string into a file usable in the pipeline.
StudyDistance 3.0 distances Calculates pairwise distances between the studies.
SVDAnalyzer 1.0 annotation, expr, sampleGroupTable report, resultTable Performs Singular Value Decomposition to gene sets to test whether a set of genes is significantly differentially expressed.
TableQuery 1.3 table1, ..., table15, tables, query, columnTypes table Executes an SQL query on CSV tables and creates a result table.
Text2CSV(Deprecated) 1.1 text csv Transforms a "dirty" csv-file into a csv-file that has a header and correctly tab-separated columns.
TextFileSplitter 1.0 file array Splits a text file (such as CSV) into an array of smaller text files.
TimeSeriesGraph 1.1 activities, linkStyles graph, legend, status, stats Provides a pathway model that could explain expression changes within a time series.
TreeSplitter 1.02 tree, nodeAnnotations newTree, splits Splits the leafs of a tree into two sets such that the mutual information between the split and leaf annotations is maximized.
TumorscapeReader 2.0 queryGenes, database features Connects to the Tumorscape database and outputs chromosomal aberration information for the query genes.
URLInput   in Imports an external input file to a workflow script from a URL source.
VariationFilter 1.1 matrix matrix Filters out rows from a matrix where the standard deviation is below (or above) a threshold.
VennDiagram 1.1.2 sets report, sets Draws Venn diagrams showing the intersections of the given sets of identifiers.
VertexJoin 1.4 graph graph, joins Simplifies the given graph by merging vertices with an equal set of edges.
WekaAPriori 1.1 data, selectedColumns rules Mines association rules using a priori algorithm: R.
WekaAttributeSelection 1.0 data selectedData Selects parameters using Weka AttributeSelection classes.
WekaClassifier 1.1 data, testdata, classifydata, classifier classifier, report, confusion, evaluation, predictedClasses Creates a classifier based on the given sample data.
WekaClusterer 1.0 data clusters Clusters data using clustering methods implemented in Weka.
WekaTransform 1.3 data transformedData Transforms data using filter classes implemented in Weka.
XML2CSV 1.2 xml csv Transforms an XML file into CSV table.
XrefLinkRule 1.0 moksiskaan refs Provides a template of World Wide Web links that can be used to map external database identifiers to resources of further information.

Function summary

Name Version Inputs Outputs Description
AffyNormalization 1.0 affy, sampleNames report Reads in Affymetrix gene expression microarrays and compares various normalization methods.
AffySNPFetch 1.0 markernames, connection rsnumbers Fetches SNP rs-numbers from Ensembl based on Affy SNP-ids.
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.
ArrayBashEvaluate 1.1 array array Applies a bash script on array items and creates a new array based on the standard output of the script.
CandidateReport 3.1 candidates, moksiskaan, ensembl, enrichmentTable, status, corrData report, bioAnnotation, candidates, pathway Produces a summary description of the given set of candidate genes.
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.
ClusterReorder 1.0 clusters, data neworder Re-orders cluster ID numbers based on a given data vector.
CorrelationGraph 1.1 pathway, data connections, stats, entities, skipped Produces a graph that represents the correlations between the activities of the bioentities within the input pathway.
DescribeStudies 1.0 moksiskaan, studies report Producers a table describing the studies of interests.
DocumentGenerator 1.1 body1, ..., body7, bibtex, abstract, appendix document Creates a PDF document from the given LaTeX elements and of the system configuration.
DrugReport 1.4 genes, status, drugs report, pathway, status Gives predictions of drugs that could target the given genes.
ECGroup 1.0 genes, moksiskaan genes Finds the Enzyme Commission numbers (EC numbers) for the given genes and performs a search for genes with similar enzymatic activity.
EnzymeSubstitution 1.0 status, moksiskaan substitutions Finds enzyme substitution pairs for a given sample profile.
ExpressionImport 0.1 datasets, sampleNames expr Reads expression data, applies all available normalization methods and returns a record with normalized datasets.
FennPathway 1.2.1 red, green, blue, status graph, report, sets Produces a pathway that illustrates the relationships between two to three given gene sets.
GenomicVariantAnnotator 2.0 inputT table Queries the Database of Genomic Variants.
GOBackground 1.2 ensembl, moksiskaan enrichment, similarity, annotations Produces the custom a priori probability tables for Gene Ontology similarity and enrichment analysis.
GOReport 1.2.1 genes, enrichmentTable, status, moksiskaan report Performs a Gene Ontology enrichment analysis and generates a report out of the results.
GOSelect 2.0 bioAnnotation, go report, hits Generates a report where the given genes are assigned to the Gene Ontologies of interest.
HistogramPlot 1.1 csv, plotAnnotator data, midpoints, plot Counts the frequencies and makes a line plot of histogram values.
InteractionPlot 1.0 interactions, expression, groups plot Plots the distribution of the expression of two genes.
LatexSearchReplace 1.0 document, rules document Transforms text (including Tex) files in the given Latex directory by replacing certain string with new values in the specified text files.
MicroarrayReader 0.7 data, sampleNames channel1, sampleAnnotation Reads in expression microarray data produced by feature extraction software.
MoksiskaanInit 1.1 connection, report Initialization of Moksiskaan environment.
QueryReport 1.2 query, table1, ..., table8, refs report, data Executes an SQL query and prints it with the result table.
RegionOverlap 1.2 regions1 regions Produces a list of overlapping DNA regions.
RGBGraph 1.1.1 graph, red, green, blue graph, legend, red, green, blue, edgeAttributes, vertexAttributes Adds red, green and blue to the nodes of the given graph.
SampleGraph 1.0 statusExpr, statusCopy, statusMeth, moksiskaan, geneScope pathway, legend, status Produces a graph that represents the connectivity of active genes for an individual.
SimilarityGraph 1.0 matrix, annotations graph Generates a clustering graph of row entities based on the column values.
TargetStatus 1.2 statuses, moksiskaan, targets statuses, roles Propagates the activity statuses of the given bioentities to their targets.
TimeSeriesReport 1.2 activities report, graph, status, stats Produces a report that includes and describes a hypothetical signalling cascade matching the time series data.
TopHits 1.6 moksiskaan scores, bioentities Ranks the hits based on the given set of studies.

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