Up: Components summary Author

Kristian Ovaska

Component Version Inputs Outputs Description
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.
AgilentReader 1.0.1 agilent, sampleNames green, green2, red, red2, probeAnnotation, sampleAnnotation, groups Imports data from microarray text files such as Agilent CSV files.
ArrayCombiner 1.1 array1, array2, array3, array4, array5, array6, array7, array8, array9, array10, array11, array12, array13, array14, array15, array16, array17, array18, array19, array20 out Combines multiple arrays into one using set operations on array keys.
ArrayConstructor 1.0 file1, file2, file3, file4, file5, file6, file7, file8, file9, file10, file11, file12, file13, file14, file15, file16, file17, file18, file19, file20, file21, file22, file23, file24, file25, file26, file27, file28, file29, file30, file31, file32, file33, file34, file35, file36, file37, file38, file39, file40, file41, file42, file43, file44, file45, file46, file47, file48, file49, file50, file51, file52, file53, file54, file55, file56, file57, file58, file59, file60, file61, file62, file63, file64, file65, file66, file67, file68, file69, file70, file71, file72, file73, file74, file75, file76, file77, file78, file79, file80, file81, file82, file83, file84, file85, file86, file87, file88, file89, file90, file91, file92, file93, file94, file95, file96, file97, file98, file99 out Constructs an array from atomic elements.
ArrayExtractor 1.0 array file1, file2, file3, file4, file5, file6, file7, file8, file9 Extracts elements from an array.
AssemblyQuality 0.1 contigs, scaffolds, reference report, contigStats, scaffoldStats, contigReferenceStats, scaffoldReferenceStats Evaluate the quality of a de novo genome assembly using a variety of metrics.
AttributeVisualizer 1.0.1 annotation, matrix report Visualizes multidimensional attributes using a heat map together with a clustering dendrogram.
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.
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.
CSV2Excel 1.3 csv, csv2, csv3, csv4, csv5, csv6, csv7, csv8, csv9, array, style, refs excelFile Converts a file from CSV format to Excel 97 format.
CSV2GraphML 1.0 in out Converts a matrix or CSV representation of a graph to GraphML.
CSVFilter 1.1.1 in, aux, includeColumnsFile out Filters columns and/or rows from CSV files using flexible criteria.
CSVJoin 1.1 in1, in2, in3, in4, inDir, in out Joins rows from two or more CSV files from all the inputs, optionally using one column as a matching key.
CSVTransformer 1.1 csv1, csv2, columnNamesFile, array out Transforms CSV files using R expressions.
DEGReport 1.1.1 deg, geneAnnotation, expr summary, genelist Creates a LaTeX report on differentially expressed genes (DEGs).
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.
DuplicateQuality 1.0 expr, geneAnnotation report Estimates microarray chip quality by printing expression distributions for duplicate probes.
EntrezAnnotator 1.0 in out Retrieves database records from NCBI Entrez, including gene annotation, PubMed references and sequences.
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.
ExpressionExtremes 1.3 in out Selects differentially expressed genes using expression values as criterion.
FoldChange 1.1 in out Selects differentially expressed genes using fold change as criterion.
Folder2Array 1.3 folder1, folder2, folder3, folder4, folder5, folder6, folder7, folder8, folder9 out Constructs an array from folder contents.
FolderExtractor 1.0 folder file1, file2, file3, file4, file5, file6, file7, file8, file9 Extracts files from a folder.
FusionMap 1.0 reads, mates fusions, fusionReads Detect genomic fusions from paired or single ended DNA-seq or RNA-seq data using FusionMap.
GeneCount 1.0 expr1, expr2, expr3, expr4, expr5, expr6, expr7, 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 out Compiles gene ID sets into CSV files that contain gene annotations and expression.
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.
GOProbabilityTable 1.0 goAnnotation similarityTable, enrichmentTable Creates custom a priori probability tables for GO similarity and enrichment analysis.
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.
GraphVisualizer 1.2 in out Creates a visualization of a graph using Graphviz.
HTMLReport 1.0 table1, table2, table3, table4, table5, mapping, matrix1, matrix2, matrix3, matrixMapping, images, imageMapping, refs, labels report Visualizes CSV files and their relationships using statically generated HTML files.
IDConvert 1.0 in, conversionTable out Converts IDs from a column in a CSV file to other type of IDs and/or combines duplicated rows into one.
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.
LatexCombiner 1.5 latex1, latex2, latex3, latex4, latex5, latex6, latex7, latex8, latex9, array, resources document Combines several LaTeX fragments into one LaTeX document.
LatexPDF 1.1 in, header, footer out, completeDocument Compiles a LaTeX document into Portable Document Format (PDF).
LimmaNormalizer 0.6 green, greenBG, red, redBG, groups logratio Normalizes two-channel and single-channel microarrays using the Bioconductor Limma package.
MatrixRank 1.0 in out Computes ranks of values in a matrix.
MatrixTranspose 1.0 in out Transposes a matrix.
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.
MutSig 1.0 variants, coverage, covariates genes, genesExcel Determine significantly mutated genes in a set of genetic variations using MutSig.
Plot2D 1.0 y, x, labels, plotAnnotator out Creates scatter, line or bar plots where Y and X coordinates come from CSV files.
QuantileFilter 1.0 in1, in2 out1, out2 Filters values from numeric matrices that are below or above quantile limits.
Randomizer 1.0 out Generates numeric matrices filled with random values.
RandomSampler 0.5 in out Randomly selects rows and columns from a text or CSV file without replacement.
RegionTransformer 0.3 regions, region_set, folder, scriptFile result, array, folder Computes DNA region set operations such as union and overlap.
SampleCombiner 1.0 in, groups out 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.
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 in 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_out Extracts SBML attributes into a CSV file, or imports attributes from a CSV file.
ScalaEvaluate 1.0 scriptFile, table1, table2, table3, table4, table5, var1, var2, var3 table, optOut1, optOut2, optOut3, scriptOut Executes a Scala script.
SetTransformer 0.6 transformation, set1, set2, set3, set4, set5 result Transforms sets using union, intersection, difference and other functions.
SGA 1.0 reads, mates contigs, scaffolds Perform de novo assembly for sequencing reads using String Graph Assembler (SGA).
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, channel2, logratio report Creates spatial plots for red/green channels, log ratios and spot quality.
SPINLONG 1.0 bedFiles, patterns, regions, chromosomes, mappability, control scores, plots, patternsDump Identify user-defined spatio-temporal patterns in ChIP-seq and other sequencing data using the SPINLONG method.
StatisticalTest 1.1 matrix, matrix2, groups pvalues, idlist Computes p-values using statistical tests, optionally with correction for multiple hypotheses.
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.
TextFileSplitter 1.0 in out Splits a text file (such as CSV) into an array of smaller text files.
VariationFilter 1.1 in out Filters out rows from a matrix where the standard deviation is below (or above) a threshold.
VennDiagram 1.1.2 in report, out Draws Venn diagrams showing the intersections of the given sets of identifiers.

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