Analysis of Copy Number Variation in Single-Cell-Sequencing Data

aneuBiHMM | Bivariate Hidden Markov Model |

Aneufinder | Wrapper function for the 'AneuFinder' package |

AneuFinder-package | Copy-number detection in WGSCS and Strand-Seq data |

aneuHMM | Hidden Markov Model |

annotateBreakpoints | Annotate breakpoints |

bam2GRanges | Import BAM file into GRanges |

bed2GRanges | Import BED file into GRanges |

biDNAcopy.findCNVs | Find copy number variations (DNAcopy, bivariate) |

bi.edivisive.findCNVs | Find copy number variations (edivisive, bivariate) |

biHMM.findCNVs | Find copy number variations (bivariate) |

binned.data | Binned read counts |

binning | Bin the genome |

binReads | Convert aligned reads from various file formats into read... |

blacklist | Make a blacklist for genomic regions |

clusterByQuality | Cluster based on quality variables |

clusterHMMs | Cluster objects |

collapseBins | Collapse consecutive bins |

colors | 'AneuFinder' color scheme |

compareMethods | Compare copy number calling methods |

compareModels | Compare copy number models |

consensusSegments | Make consensus segments |

correctGC | GC correction |

DNAcopy.findCNVs | Find copy number variations (DNAcopy, univariate) |

edivisive.findCNVs | Find copy number variations (edivisive, univariate) |

estimateComplexity | Estimate library complexity |

export | Export genome browser viewable files |

filterSegments | Filter segments by minimal size |

findCNVs | Find copy number variations |

findCNVs.strandseq | Find copy number variations (strandseq) |

findHotspots | Find breakpoint hotspots |

fixedWidthBins | Make fixed-width bins |

getBreakpoints | Extract breakpoints |

getDistinctColors | Get distinct colors |

getQC | Obtain a data.frame with quality metrics |

getSCEcoordinates | Get SCE coordinates |

heatmapAneuploidies | Plot aneuploidy state |

heatmapGenomewide | Genome wide heatmap of CNV-state |

heatmapGenomewideClusters | Plot heatmaps for quality control |

HMM.findCNVs | Find copy number variations (univariate) |

hotspotter | Find hotspots of genomic events |

hotspotter.variable | 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 |

mergeStrandseqFiles | Merge Strand-seq libraries |

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 |

plot.GRangesList | Plotting function for binned read counts (list) |

plotHeterogeneity | Heterogeneity vs. Aneuploidy |

plotHistogram | Plot a histogram of binned read counts with fitted mixture... |

plotKaryogram | Karyogram-like chromosome overview |

plot_pca | Perform a PCA for copy number profiles |

plotProfile | Read count and CNV profile |

print.aneuBiHMM | Print aneuBiHMM object |

print.aneuHMM | Print aneuHMM object |

qualityControl | Quality control measures for binned read counts |

readConfig | Read AneuFinder configuration file |

refineBreakpoints | Refine breakpoints |

simulateReads | Simulate reads from genome |

subsetByCNVprofile | Get IDs of a subset of models |

transCoord | Transform genomic coordinates |

variableWidthBins | Make variable-width bins |

writeConfig | Write AneuFinder configuration file |

zinbinom | The Zero-inflated Negative Binomial Distribution |

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