API for csoneson/compcodeR
RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
| Global functions | |
|---|---|
| DESeq2.createRmd | Man page Source code |
| DESeq2.length.createRmd | Man page Source code |
| DSS.createRmd | Man page Source code |
| EBSeq.createRmd | Man page Source code |
| NBPSeq.createRmd | Man page Source code |
| NB_to_PLN | Man page Source code |
| NOISeq.prenorm.createRmd | Man page Source code |
| TCC.createRmd | Man page Source code |
| add_replicates | Man page Source code |
| baySeq.createRmd | Source code |
| checkClass | Source code Source code |
| checkCompatibility | Source code |
| checkDataObject | Man page Source code |
| checkParamMatrix | Man page Source code |
| checkParamVector | Man page Source code |
| checkRange | Source code |
| checkSpecies | Man page Source code |
| checkTableConsistency | Man page Source code |
| check_compData | Man page Source code |
| check_compData_results | Man page Source code |
| check_phyloCompData | Man page Source code |
| compData | Man page Source code |
| compData-class | Man page |
| compcodeR | Man page |
| compcodeR-package | Man page |
| computeAval | Source code |
| computeCorrelation | Source code |
| computeFDR | Source code |
| computeFN | Source code |
| computeFP | Source code |
| computeFactorLengths | Man page Source code |
| computeMCC | Source code |
| computeMval | Source code |
| computeOverlap | Source code |
| computeSignal | Source code |
| computeSorensen | Source code |
| computeTN | Source code |
| computeTP | Source code |
| computeTPR | Source code |
| computeTypeIerror | Source code |
| convertListTocompData | Man page Source code |
| convertListTophyloCompData | Man page Source code |
| convertcompDataToList | Man page Source code |
| convertphyloCompDataToList | Man page Source code |
| createResultTable | Source code |
| createResultsRmdFile | Source code |
| createSelectionPanel | Source code |
| definePlotColors | Source code |
| doSaveResultsTable | Source code |
| edgeR.GLM.createRmd | Man page Source code |
| edgeR.exact.createRmd | Man page Source code |
| extract_results_phylolm | Man page Source code |
| findFileIdx | Source code |
| findGenesAllZero | Source code |
| generateCodeHTMLs | Man page Source code |
| generateLengths | Man page Source code |
| generateLengthsPhylo | Man page Source code |
| generateSyntheticData | Man page Source code |
| getNegativeBinomialDispersion | Man page Source code |
| getNegativeBinomialMean | Man page Source code |
| getNegativeBinomialParameters | Man page Source code |
| getTree | Man page Source code |
| get_factor | Source code |
| get_model_factor | Man page Source code |
| get_poisson_log_normal_parameters | Man page Source code |
| lengthNorm.limma.createRmd | Man page Source code |
| lengthNorm.sva.limma.createRmd | Man page Source code |
| listcreateRmd | Man page Source code |
| logcpm.limma.createRmd | Man page Source code |
| makeFalseDiscoveryCurves | Source code |
| makeROCcurves | Source code |
| nEffNaive | Man page Source code |
| nEffPhylolm | Source code |
| nEffRatio | Man page Source code |
| nEffSchur | Source code |
| padResultTable | Source code |
| performComparison | Source code |
| phyloCompData | Man page Source code |
| phyloCompData-class | Man page |
| phyloCompDataFromCompData | Man page Source code |
| phylolm.createRmd | Man page Source code |
| phylolm_analysis | Man page Source code |
| plotFDRVsExpr | Source code |
| plotMASignificant | Source code |
| plotResultTable | Source code |
| plotScoreVsExpr | Source code |
| plotScoreVsOutliers | Source code |
| plotSignalForZeroCounts | Source code |
| prune_tree_one_obs | Source code |
| runComparison | Man page Source code |
| runComparisonGUI | Man page Source code |
| runComparisonShiny | Man page Source code |
| runDiffExp | Man page Source code |
| scale_variance_process | Man page Source code |
| shorten.method.names | Source code |
| show,compData-method | Man page |
| show,phyloCompData-method | Man page |
| show_compData | Man page Source code |
| simulateData | Man page Source code |
| simulateDataPhylo | Man page Source code |
| simulatePhyloPoissonLogNormal | Man page Source code |
| sqrtcpm.limma.createRmd | Man page Source code |
| summarizeSyntheticDataSet | Man page Source code |
| trim_tree | Source code |
| ttest.createRmd | Man page Source code |
| voom.limma.createRmd | Man page Source code |
| voom.ttest.createRmd | Man page Source code |
| writeNormalization | Man page Source code |
