| Component |
Version |
Inputs |
Outputs |
Description |
| Ascat |
1.3 |
tumorLogR, tumorBAF, controlLogR, controlBAF, gcContent, gender |
results, summary, intermediate, plots |
Runs Allele specific copy number analysis with ploidy and tumor purity estimation using the tool ASCAT. |
| BICseq |
1.0 |
test, control |
results, calls, cloneCalls |
Detects copy number alterations from whole-genome sequencing data using BICseq
tool. |
| CombinationCounter |
1.1 |
in |
out, ratios |
Count the occurrencies of combinations of two labels. |
| CSVDplyr |
1.2 |
csv1, csv2, csv3, in |
out |
Applies up to R functions (including dplyr functions) to the input csv1. |
| CSVSummary |
1.1 |
in |
out |
Summarises values for rows of a file according to a column label or the whole file to single row. |
| ExpressionQuantifier |
2.0 |
alignment, reference, referenceFolder, annotation, mask, array |
folder, genes, isoforms |
Quantifies expression from a bam file from RNA-Seq. |
| 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. |
| FusionAnalyzer |
1.0 |
in, csvs |
out, folder |
Post-processing tool for gene fusion analysis. |
| GenomeSlider |
1.0 |
matrix, regions, chrLengths |
regionsSummary, windowsSummary |
Summarized genomic events at sliding window intervals and/or at predifined regions. |
| 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. |
| KaplanMeierPlot |
1.0 |
in |
plots, plotObject, survPvalue, CoxStats |
Plots Kaplan Meier survival plot using the survival and survminer R packages. |
| LiftOver |
1.1 |
regions, chain |
out |
Converts chromosome region coordinates from one genome build to another. |
| PairCorrelation |
1.1 |
data, pairs |
stats, skipped |
Calculates correlations for the row pairs. |
| PanelDoc |
1.0 |
|
bedgraph, calls, raw, normalized, PDFs, QC_Metrics, General_output, CNVPanelizer_results |
Calls CNV ratios/gains/losses using the existing programs PanelDoc (developed by Nord et al. 2011) or CNVPanelizer (Bioconductor package), or both, with custom filtering available. |
| PanelDoc |
1.0 |
|
bedgraph, calls, raw, normalized, PDFs, QC_Metrics, General_output, CNVPanelizer_results |
Calls CNV ratios/gains/losses using the existing programs PanelDoc (developed by Nord et al. 2011) or CNVPanelizer (Bioconductor package), or both, with custom filtering available. |
| PointDistance |
1.1 |
in, reference |
out |
Measures the nearest reference point (reference) distance for each input point (in). |
| PopulationTimeline |
1.0 |
in |
out |
Currently it uses Wanderlust to calculate developmental trajectories within a population of single cell data. |
| PyClone |
0.1 |
in, purity |
config, trace, mutationFiles, clusteringResults |
Component to run PyClone variant clustering tool. |
| PyCloneQC |
1.0 |
config, trace, mutationFiles |
corr, conv, plots |
Quality checker for PyClone variant clustering tool. |
| PyCloneRC |
1.0 |
config, trace, mutationFiles |
clusteringResults, plots |
Reclustering tool for PyClone variant clustering. |
| 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. |
| RNAVariantCaller |
1.0 |
reference, in |
out |
Variant calling in RNAseq data using HaplotypeCaller and VariantFiltration in GATK. |
| SignatureExtractor |
1.2 |
in |
outContribution, outNmuation, signatureDistance, plots |
This component performs signature extraction from point mutation data using non-negative matrix factorization following the pipeline in SomaticSignature R package. |
| StatisticalTest |
1.1 |
matrix, matrix2, groups |
pvalues, idlist |
Computes p-values using statistical tests, optionally with correction for
multiple hypotheses. |
| SubsetBam |
1.0 |
in, annotation |
out |
Extracts reads from a BAM file based on chromosomal regions specified by a user and produces
a merged BAM file containing only those regions. |
| 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. |
| WekaAPriori |
1.1 |
in, selectedColumns |
out |
Mines association rules using a priori algorithm:
R. |
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