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 |
correctGC | GC correction |
correctMappability | Mappability correction |
deltaWCalculator | Calculate deltaWs |
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 |
findSCEs | Find sister chromatid exchanges |
fixedWidthBins | Make fixed-width bins |
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 |
loadGRangesFromFiles | Load GRanges from files |
loadHmmsFromFiles | Load HMMs from files |
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 |
plotBinnedDataHistogram | Plot a histogram of binned read counts |
plotKaryogram | Karyogram-like chromosome overview |
plotProfile | Read count and CNV profile |
plotUnivariateHistogram | Plot a histogram of binned read counts with fitted mixture distribution |
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.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 |