| 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. |
Up: Components summary
Kristian Ovaska