Up: Components summary Author

Riku Louhimo

Component Version Inputs Outputs Description
ACGHnorm 1.4 caseIn, control, admixtureMatrix, probeAnnotation casechannel, controlchannel, fit Normalizes two channel array CGH data with LOESS, median or mode.
ACGHsegment 2.0 caseChan, geneAnnotation report, segments, tholds, lossProbs, gainProbs, normProbs, rawSegments, frequency Segments Array CGH data with the Circular Binary Segmentation (CBS) algorithm and produces hard or soft copy number aberration calls.
AffySNPFetch 1.0 markernames, connection rsnumbers Fetches SNP rs-numbers from Ensembl based on Affy SNP-ids.
Bam2Counts 0.8 in out Converts Bam files to count matrices summarizing on gene, transcript or exon level.
CircosPlot 0.7 data, data2, data3, data4, data5, data6, data7, data8, data9, data10, data11, dataAnnotation, plotAnnotation, links, highlights, plotParams, karyotype circos, ideogram, ticks, plot Draws circos plots from genomic data.
CN2GECollection 1.0 exprMatrix, cnaMatrix, exprAnnotation, exprRefMatrix, cnaRefMatrix, labels concomitantGenes, concomitantGenes2, plot Encapsulates three algorithms with similar inputs for copy number to RNA expression integration.
CNACaller 1.0 segments, probeAnnotation regions Calls significant copy number alterations from a group of segmented copy number alteration profiles.
CNGEIntegrator 1.1.0 CNAProbLoss, CNAProbGain, CNAProbNorm, exprMatrix, exprAnnotation integrationResult Performs one of two possible nonparametric tests for the detection of copy number induced differential gene expression.
EdgeR 1.0 counts, groups, reads logratio, plot, normalized Computes the digital expression fold change and p-value based on counts.
EncodeTextFile 0.1 in out Convert general text files from one character encoding to another.
EnsemblChromosomes 1.0 connection chromosomes, extraChr Retrieves the Ensembl names and lengths of chromosomes.
ExonAnnotator 1.0 query, dbConnect table Maps gene, transcript or exon Ensembl IDs to one another via the Ensembl query interface.
ExpExpIntegration 1.1 labelMatrix, exprMatrix Values Integrates gene/transcript/other expression data with binary explanatory data derived in some way.
ExprMethylCGH 1.1.1 exprMatrix, cghMatrix, methylMatrix statistics Integrates expression data with methylation and CGH data by using two label matrices of ones and zeros.
GenomicRearrangement 0.1 reference, input, folder delly Call genomic rearrangments.
GenomicVariantAnnotator 2.0 inputT table Queries the Database of Genomic Variants.
GSVDIntegrator 1.0.1 exprMatrix, cnaMatrix, exprAnnotation integrationResults, cghResults, annotations Extracts variation patterns from two matrices based on the generalized singular value decomposition.
HeatMapReport 3.0 in, rowLabels, colLabels out Clusters samples hierarchically and draws the corresponding dendrograms and heat map.
IlluminaAnnotator 13.10 in out Fetches genomic annotations for Illumina methylation and expression array probes.
KaplanMeier 2.2 survival, annotation report, statistics, plots Produces a Kaplan-Meier plot representing survival estimates based on the given data.
MicroarrayReader 0.7 data, sampleNames channel1, channel2, sampleAnnotation Reads in expression microarray data produced by feature extraction software.
MutationContextPlot 0.1 array, in plot Draws mutation context plots for sequencing samples.
RowJoin 0.5 matrix, thresholds table Joins duplicate id rows from a numeric matrix based on the frequency of some given value.
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.
SegmentPlot 1.5 chrSegments plot, SignRegion Plots segmented chromosomal data.
SNPArrayReader 1.7 dataDir, sampleNames genotypeMatrix, markerNames, copynumberMatrix, probeAnnotation Imports genotype data from Illumina SNP and Affymetrix SNP 6.0 or 5.0 files.
SNPKaplanMeier 1.6.1 genotypes, survival, annotations statistics, report Calculates Kaplan-Meier estimates for genotype specific survival effects.
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.
TumorscapeReader 2.0 queryGenes, database features Connects to the Tumorscape database and outputs chromosomal aberration information for the query genes.
VariantCaller 1.0 reference, bam1, bam2, bams, intervals, dbsnp snp, indel, metrics

Calls genomic sites of variation using the specified caller.

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