Man pages for ataudt/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
annotateBreakpointsAnnotate breakpoints
bam2GRangesImport BAM file into GRanges
bed2GRangesImport BED file into GRanges
biDNAcopy.findCNVsFind copy number variations (DNAcopy, bivariate)
bi.edivisive.findCNVsFind copy number variations (edivisive, bivariate)
biHMM.findCNVsFind copy number variations (bivariate)
binned.dataBinned read counts
binningBin the genome
binReadsConvert aligned reads from various file formats into read...
blacklistMake a blacklist for genomic regions
clusterByQualityCluster based on quality variables
clusterHMMsCluster objects
collapseBinsCollapse consecutive bins
colors'AneuFinder' color scheme
compareMethodsCompare copy number calling methods
compareModelsCompare copy number models
consensusSegmentsMake consensus segments
correctGCGC correction
DNAcopy.findCNVsFind copy number variations (DNAcopy, univariate)
edivisive.findCNVsFind copy number variations (edivisive, univariate)
estimateComplexityEstimate library complexity
exportExport genome browser viewable files
filterSegmentsFilter segments by minimal size
findCNVsFind copy number variations
findCNVs.strandseqFind copy number variations (strandseq)
findHotspotsFind breakpoint hotspots
fixedWidthBinsMake fixed-width bins
getBreakpointsExtract breakpoints
getDistinctColorsGet distinct colors
getQCObtain a data.frame with quality metrics
getSCEcoordinatesGet SCE coordinates
heatmapAneuploidiesPlot aneuploidy state
heatmapGenomewideGenome wide heatmap of CNV-state
heatmapGenomewideClustersPlot heatmaps for quality control
HMM.findCNVsFind copy number variations (univariate)
hotspotterFind hotspots of genomic events
hotspotter.variableFind hotspots of genomic events
importBedRead bed-file into GRanges
initializeStatesInitialize state factor levels and distributions
karyotypeMeasuresMeasures for Karyotype Heterogeneity
loadFromFilesLoad 'AneuFinder' objects from file
mergeStrandseqFilesMerge Strand-seq libraries
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
plot.GRangesListPlotting function for binned read counts (list)
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
refineBreakpointsRefine breakpoints
simulateReadsSimulate reads from genome
subsetByCNVprofileGet IDs of a subset of models
transCoordTransform genomic coordinates
variableWidthBinsMake variable-width bins
writeConfigWrite AneuFinder configuration file
zinbinomThe Zero-inflated Negative Binomial Distribution
ataudt/aneufinder documentation built on Nov. 21, 2018, 10:10 a.m.