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| AneuFinder-package | Copy-number detection in WGSCS and Strand-Seq data |
| aneuBiHMM | Bivariate Hidden Markov Model |
| AneuFinder | Copy-number detection in WGSCS and Strand-Seq data |
| Aneufinder | Wrapper function for the 'AneuFinder' package |
| aneuHMM | Hidden Markov Model |
| bam2GRanges | Import BAM file into GRanges |
| bed2GRanges | Import BED file into GRanges |
| binned.data | Binned read counts |
| binning | Bin the genome |
| binReads | Convert aligned reads from various file formats into read counts in equidistant bins |
| bivariate.findCNVs | Find copy number variations (bivariate) |
| blacklist | Make a blacklist for genomic regions |
| clusterByQuality | Cluster based on quality variables |
| collapseBins | Collapse consecutive bins |
| colors | 'AneuFinder' color scheme |
| compareMethods | Compare copy number calling methods |
| compareModels | Compare copy number models |
| correctGC | GC correction |
| correctMappability | Mappability correction |
| deltaWCalculator | Calculate deltaWs |
| DNAcopy.findCNVs | Find copy number variations (DNAcopy) |
| dzinbinom | The Zero-inflated Negative Binomial Distribution |
| estimateComplexity | Estimate library complexity |
| export | Export genome browser viewable files |
| exportCNVs | Export genome browser viewable files |
| exportGRanges | Export genome browser viewable files |
| exportReadCounts | Export genome browser viewable files |
| filterSegments | Filter segments by minimal size |
| findCNVs | Find copy number variations |
| findCNVs.strandseq | Find copy number variations (strandseq) |
| fixedWidthBins | Make fixed-width bins |
| getQC | Obtain a data.frame with quality metrics |
| getSCEcoordinates | Get SCE coordinates |
| getSegments | Extract segments and cluster |
| heatmapAneuploidies | Plot aneuploidy state |
| heatmapGenomewide | Genome wide heatmap of CNV-state |
| hotspotter | Find hotspots of genomic events |
| importBed | Read bed-file into GRanges |
| initializeStates | Initialize state factor levels and distributions |
| karyotypeMeasures | Measures for Karyotype Heterogeneity |
| loadFromFiles | Load 'AneuFinder' objects from file |
| plot.aneuBiHMM | Plotting function for 'aneuBiHMM' objects |
| plot.aneuHMM | Plotting function for 'aneuHMM' objects |
| plot.character | Plotting function for saved 'AneuFinder' objects |
| plot.GRanges | Plotting function for binned read counts |
| plotHeterogeneity | Heterogeneity vs. Aneuploidy |
| plotHistogram | Plot a histogram of binned read counts with fitted mixture distribution |
| plotKaryogram | Karyogram-like chromosome overview |
| plotProfile | Read count and CNV profile |
| pzinbinom | The Zero-inflated Negative Binomial Distribution |
| qc.bhattacharyya | Quality control measures for binned read counts |
| qc.entropy | Quality control measures for binned read counts |
| qc.sos | Quality control measures for binned read counts |
| qc.spikiness | Quality control measures for binned read counts |
| qualityControl | Quality control measures for binned read counts |
| qzinbinom | The Zero-inflated Negative Binomial Distribution |
| readConfig | Read AneuFinder configuration file |
| rzinbinom | The Zero-inflated Negative Binomial Distribution |
| simulateReads | Simulate reads from genome |
| stateColors | 'AneuFinder' color scheme |
| strandColors | 'AneuFinder' color scheme |
| subsetByCNVprofile | Get IDs of a subset of models |
| transCoord | Transform genomic coordinates |
| univariate.findCNVs | Find copy number variations (univariate) |
| variableWidthBins | Make variable-width bins |
| writeConfig | Write AneuFinder configuration file |
| zinbinom | The Zero-inflated Negative Binomial Distribution |