| Component |
Version |
Inputs |
Outputs |
Description |
| BoxPlot |
1.3.1 |
in1, in2, in3, groups, dataPoints |
out |
Creates box plots for numeric data. |
| 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. |
| CSV2Latex |
2.3 |
tabledata, refs |
report |
Converts the given comma separated value file to a LaTeX table. |
| 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. |
| 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. |
| 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. |
| IlluminaPlot |
1.1 |
in |
out |
Produces quality control plots. |
| KaplanMeier |
2.2 |
survival, annotation |
report, statistics, plots |
Produces a Kaplan-Meier plot representing survival estimates based on the given data. |
| 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. |
| LatexPDF |
1.1 |
in, header, footer |
out, completeDocument |
Compiles a LaTeX document into Portable Document Format (PDF). |
| LatexSearchReplace |
1.0 |
in, rules |
out |
Transforms text (including Tex) files in the given Latex directory by replacing certain string with
new values in the specified text files. |
| 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. |
| Logo |
1.6 |
motifs, annot, subset |
report |
Generates sequence logos for the given DNA motifs. |
| MatlabEvaluate |
1.0 |
script, table1, table2, table3, table4, table5, var1, var2, var3, var4, var5, var6, var7, var8, var9 |
table, optOut1, optOut2, optOut3, document |
Executes a Matlab script that generates a matrix from the given data. |
| MDSPlot |
2.2 |
expr, groups |
mdsCoOrdinates, report |
Plots multidimensional scaling of numeric data. |
| 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. |
| 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. |
| SegmentPlot |
1.5 |
chrSegments |
plot, SignRegion |
Plots segmented chromosomal data. |
| 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). |
| SpatialPlot |
1.4 |
geneAnnotation, channel1, channel2, logratio |
report |
Creates spatial plots for red/green channels, log ratios
and spot quality. |
| SyntaxHighlight |
1.1 |
in |
HTML, image, latex |
Reads a program code listing, and creates a syntax highlighted HTML file. |
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Latex