Man pages for Bioconductor-mirror/AneuFinder
Analysis of Copy Number Variation in Single-Cell-Sequencing Data

aneuBiHMMBivariate Hidden Markov Model
AneufinderWrapper function for the 'AneuFinder' package
AneuFinder-packageCopy-number detection in WGSCS and Strand-Seq data
aneuHMMHidden Markov Model
bam2GRangesImport BAM file into GRanges
bed2GRangesImport BED file into GRanges
biDNAcopy.findCNVsFind copy number variations (DNAcopy, bivariate)
binned.dataBinned read counts
binningBin the genome
binReadsConvert aligned reads from various file formats into read...
bivariate.findCNVsFind copy number variations (bivariate)
blacklistMake a blacklist for genomic regions
clusterByQualityCluster based on quality variables
collapseBinsCollapse consecutive bins
colors'AneuFinder' color scheme
compareMethodsCompare copy number calling methods
compareModelsCompare copy number models
consensusSegmentsMake consensus segments
correctGCGC correction
correctMappabilityMappability correction
deltaWCalculatorCalculate deltaWs
DNAcopy.findCNVsFind copy number variations (DNAcopy, univariate)
estimateComplexityEstimate library complexity
exportExport genome browser viewable files
filterSegmentsFilter segments by minimal size
findBreakpointsFind breakpoints
findCNVsFind copy number variations
findCNVs.strandseqFind copy number variations (strandseq)
fixedWidthBinsMake fixed-width bins
getDistinctColorsGet distinct colors
getQCObtain a data.frame with quality metrics
getSCEcoordinatesGet SCE coordinates
getSegmentsExtract segments and cluster
heatmapAneuploidiesPlot aneuploidy state
heatmapGenomewideGenome wide heatmap of CNV-state
heatmapGenomewideClustersPlot heatmaps for quality control
hotspotterFind hotspots of genomic events
importBedRead bed-file into GRanges
initializeStatesInitialize state factor levels and distributions
karyotypeMeasuresMeasures for Karyotype Heterogeneity
loadFromFilesLoad 'AneuFinder' objects from file
plot.aneuBiHMMPlotting function for 'aneuBiHMM' objects
plot.aneuHMMPlotting function for 'aneuHMM' objects
plot.characterPlotting function for saved 'AneuFinder' objects
plot.GRangesPlotting function for binned read counts
plotHeterogeneityHeterogeneity vs. Aneuploidy
plotHistogramPlot a histogram of binned read counts with fitted mixture...
plotKaryogramKaryogram-like chromosome overview
plot_pcaPerform a PCA for copy number profiles
plotProfileRead count and CNV profile
print.aneuBiHMMPrint aneuBiHMM object
print.aneuHMMPrint aneuHMM object
qualityControlQuality control measures for binned read counts
readConfigRead AneuFinder configuration file
simulateReadsSimulate reads from genome
subsetByCNVprofileGet IDs of a subset of models
transCoordTransform genomic coordinates
univariate.findCNVsFind copy number variations (univariate)
variableWidthBinsMake variable-width bins
writeConfigWrite AneuFinder configuration file
zinbinomThe Zero-inflated Negative Binomial Distribution
Bioconductor-mirror/AneuFinder documentation built on May 28, 2017, 11:07 p.m.