Up: Components summary
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. |