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Analysis

Description Data analysis components.
Child categories
Classification ClassifierPerformance EnsembleAttributeSelection GMLVQClassifier SampleBalancer WekaClassifier
Clustering AttributeVisualizer GOClustering BackSPIN BayesianBiclustering BiclustClusterer ClusterReorder ClusterReport FSomMetaClustering ISABiclust LinearBinner PhenographClusterer QUBICClusterer WekaClusterer XShiftClusterer ClusterAnnotator
Convert CSV2FASTA KeywordMatcher Bam2Counts Bam2Fastq FASTA2CSV CSV2Excel CSV2IDList CSV2JSON CSV2Latex CSV2SetList CSVCleaner CSVColRename CSVJoin CSVListJoin CSVSplit CSVSplitColumns EncodeTextFile Excel2CSV Excel2Text ExpandCollapse ExtensiveCSVJoin FolderExtractor IDConvert JCSVJoin Labels2Columns MatrixTranspose Properties2Latex RowJoin SearchReplace SetTransformer SourceCode2Latex SyntaxHighlight TableQuery WekaAttributeSelection WekaTransform LatexSearchReplace
Copy Number Analysis ACGHnorm ACGHsegment CN2GECollection CNACaller CNGEIntegrator SegmentPlot RUBIC
DEG DEGReport ExpressionExtremes ExprMixtureModel FoldChange CreateSQLiteIDs DEan SampleExpression
Exon DEE2DEG ExonAnnotator ExonExpression ExonToPeptide
GO GOClustering GOEnrichment GOFilter GOProbabilityTable GOSearch GSEAAnalyzer KorvasieniAnnotator
Graph KGML2GraphML CSV2GraphML Directed2Undirected GraphAnnotator GraphMetrics GraphSplitter GraphVisualizer TreeSplitter VertexJoin
Integration CN2GECollection CNGEIntegrator ExpExpIntegration ExprMethylCGH GSVDIntegrator GlobalCorrelation MirMatch TPquery DataOverlap
Meap LimmaStat MeapNormalization MeapQuantification MeapVisualizer
Multivariate Statistics PCA QSNE TSNE
Pathway GSEAAnalyzer KGML2GraphML SigPathway SPIA SVDAnalyzer ModelicaCompiler ModelicaSimulator SBML2GraphML SBML2HTML SBMLSimulator SBMLTable
Sequence Motif JASPARMotif Logo MEMERunner MotifMatch RNAFold
Short-read Sequencing MACS NextGene PeakScore RegionReport DESeqExpr GenomicRearrangement SPINLONG RegionOverlap FusionMap
SNP AlleleCounter GenotypeComparator MarkerCorrelations NextGene Plink RefSNPAnnotator SNPArrayReader SNPHelistinReader SNPKaplanMeier AffySNPFetch
Survival SNPKaplanMeier KaplanMeier
DNA Methylation BismarkAlign BSAlign DiffMeth DMML MethFilterNorm MethylCall MethylExtract SelectDiffMeth SelectMethContext
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.
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.
UMIQuantifier 1.0 alignment, annotation folder, rmdupAlignment, table, corrected Quantifies distinct unique molecular identifiers (UMIs) from a bam file.
WekaAPriori 1.1 in, selectedColumns out Mines association rules using a priori algorithm: R.

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