AneuFinder: Analysis of Copy Number Variation in Single-Cell-Sequencing Data
Version 1.4.0

This package implements functions for CNV calling, plotting, export and analysis from whole-genome single cell sequencing data.

AuthorAaron Taudt, Bjorn Bakker, David Porubsky
Bioconductor views CopyNumberVariation GenomicVariation HiddenMarkovModel Software WholeGenome
Date of publicationNone
MaintainerAaron Taudt <aaron.taudt@gmail.com>
LicenseArtistic-2.0
Version1.4.0
URL https://github.com/ataudt/aneufinder.git
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("AneuFinder")

Getting started

Package overview
README.md

Popular man pages

AneuFinder-package: Copy-number detection in WGSCS and Strand-Seq data
bed2GRanges: Import BED file into GRanges
biDNAcopy.findCNVs: Find copy number variations (DNAcopy, bivariate)
binReads: Convert aligned reads from various file formats into read...
blacklist: Make a blacklist for genomic regions
clusterByQuality: Cluster based on quality variables
print.aneuBiHMM: Print aneuBiHMM object
See all...

All man pages Function index File listing

Man pages

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
bam2GRanges: Import BAM file into GRanges
bed2GRanges: Import BED file into GRanges
biDNAcopy.findCNVs: Find copy number variations (DNAcopy, bivariate)
binned.data: Binned read counts
binning: Bin the genome
binReads: Convert aligned reads from various file formats into read...
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
consensusSegments: Make consensus segments
correctGC: GC correction
correctMappability: Mappability correction
deltaWCalculator: Calculate deltaWs
DNAcopy.findCNVs: Find copy number variations (DNAcopy, univariate)
estimateComplexity: Estimate library complexity
export: Export genome browser viewable files
filterSegments: Filter segments by minimal size
findBreakpoints: Find breakpoints
findCNVs: Find copy number variations
findCNVs.strandseq: Find copy number variations (strandseq)
fixedWidthBins: Make fixed-width bins
getDistinctColors: Get distinct colors
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
heatmapGenomewideClusters: Plot heatmaps for quality control
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...
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
simulateReads: Simulate reads from genome
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

Functions

AneuFinder Man page
AneuFinder-package Man page
Aneufinder Man page Source code
DNAcopy.findCNVs Man page Source code
aneuBiHMM Man page
aneuHMM Man page
bam2GRanges Man page Source code
bed2GRanges Man page Source code
biDNAcopy.findCNVs Man page Source code
binReads Man page Source code
binned.data Man page
binning Man page
bivariate.findCNVs Man page Source code
blacklist Man page Source code
check.integer Source code
check.logical Source code
check.multivariate.model Source code
check.nonnegative.integer.vector Source code
check.nonnegative.vector Source code
check.positive Source code
check.positive.integer Source code
check.positive.integer.vector Source code
check.positive.vector Source code
check.strand Source code
check.univariate.model Source code
check.univariate.modellist Source code
clusterByQuality Man page Source code
collapseBins Man page Source code
colors Man page
compareMethods Man page Source code
compareModels Man page Source code
consensusSegments Man page Source code
correctGC Man page Source code
correctMappability Man page Source code
dbinom.mean Source code
dbinom.prob Source code
dbinom.size Source code
dbinom.variance Source code
deltaWCalculator Man page Source code
dgeom.mean Source code
dgeom.variance Source code
dnbinom.mean Source code
dnbinom.prob Source code
dnbinom.size Source code
dnbinom.variance Source code
dzinbinom Man page Source code
estimateComplexity Man page Source code
export Man page
exportCNVs Man page Source code
exportGRanges Man page Source code
exportReadCounts Man page Source code
filterSegments Man page Source code
findBreakpoints Man page Source code
findCNVs Man page Source code
findCNVs.strandseq Man page Source code
fixedWidthBins Man page Source code
getDistinctColors Man page Source code
getQC Man page Source code
getSCEcoordinates Man page Source code
getSegments Man page Source code
get_rightxlim Source code
heatmapAneuploidies Man page Source code
heatmapGenomewide Man page Source code
heatmapGenomewideClusters Man page Source code
hotspotter Man page Source code
importBed Man page Source code
initializeStates Man page Source code
insertchr Source code
karyotypeMeasures Man page Source code
loadFromFiles Man page Source code
messageU Source code
mixedorder Source code
mixedsort Source code
onAttach Source code
plot.GRanges Man page Source code
plot.aneuBiHMM Man page Source code
plot.aneuHMM Man page Source code
plot.character Man page Source code
plot.karyogram Source code
plot.profile Source code
plotBivariateHistograms Source code
plotHeterogeneity Man page Source code
plotHistogram Man page Source code
plotKaryogram Man page Source code
plotProfile Man page Source code
plot_pca Man page Source code
print.aneuBiHMM Man page Source code
print.aneuHMM Man page Source code
pzinbinom Man page Source code
qc.bhattacharyya Man page Source code
qc.entropy Man page Source code
qc.sos Man page Source code
qc.spikiness Man page Source code
qualityControl Man page
qzinbinom Man page Source code
readConfig Man page Source code
rzinbinom Man page Source code
simulateReads Man page Source code
startTimedMessage Source code
stateColors Man page Source code
stopTimedMessage Source code
strandColors Man page Source code
stripchr Source code
subsetByCNVprofile Man page Source code
transCoord Man page Source code
univariate.findCNVs Man page Source code
variableWidthBins Man page Source code
writeConfig Man page Source code
zinbinom Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/Aneufinder.R
R/aneufinder-package.R
R/bedimport.R
R/binReads.R
R/blacklist.R
R/checkUserInput.R
R/collapseBins.R
R/compareMethods.R
R/consensusSegments.R
R/correctionMethods.R
R/dnbinom.R
R/documented_objects.R
R/export.R
R/findBreakpoints.R
R/findCNVs.R
R/findSCEs.R
R/getDistinctColors.R
R/getSegments.R
R/global.R
R/gtools.R
R/hotspotter.R
R/importReads.R
R/initializeStates.R
R/karyotypeMeasures.R
R/loadFromFiles.R
R/makeBins.R
R/plotting.R
R/printMethods.R
R/qualityMeasures.R
R/refine_changepoints.R
R/rwConfig.R
R/simulateReads.R
R/startup.R
R/timedMessage.R
R/zinbinom.R
README.md
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/AneuFinder.R
inst/doc/AneuFinder.Rnw
inst/doc/AneuFinder.pdf
man
man/AneuFinder-package.Rd
man/Aneufinder.Rd
man/DNAcopy.findCNVs.Rd
man/aneuBiHMM.Rd
man/aneuHMM.Rd
man/bam2GRanges.Rd
man/bed2GRanges.Rd
man/biDNAcopy.findCNVs.Rd
man/binReads.Rd
man/binned.data.Rd
man/binning.Rd
man/bivariate.findCNVs.Rd
man/blacklist.Rd
man/clusterByQuality.Rd
man/collapseBins.Rd
man/colors.Rd
man/compareMethods.Rd
man/compareModels.Rd
man/consensusSegments.Rd
man/correctGC.Rd
man/correctMappability.Rd
man/deltaWCalculator.Rd
man/estimateComplexity.Rd
man/export.Rd
man/filterSegments.Rd
man/findBreakpoints.Rd
man/findCNVs.Rd
man/findCNVs.strandseq.Rd
man/fixedWidthBins.Rd
man/getDistinctColors.Rd
man/getQC.Rd
man/getSCEcoordinates.Rd
man/getSegments.Rd
man/heatmapAneuploidies.Rd
man/heatmapGenomewide.Rd
man/heatmapGenomewideClusters.Rd
man/hotspotter.Rd
man/importBed.Rd
man/initializeStates.Rd
man/karyotypeMeasures.Rd
man/loadFromFiles.Rd
man/plot.GRanges.Rd
man/plot.aneuBiHMM.Rd
man/plot.aneuHMM.Rd
man/plot.character.Rd
man/plotHeterogeneity.Rd
man/plotHistogram.Rd
man/plotKaryogram.Rd
man/plotProfile.Rd
man/plot_pca.Rd
man/print.aneuBiHMM.Rd
man/print.aneuHMM.Rd
man/qualityControl.Rd
man/readConfig.Rd
man/simulateReads.Rd
man/subsetByCNVprofile.Rd
man/transCoord.Rd
man/univariate.findCNVs.Rd
man/variableWidthBins.Rd
man/writeConfig.Rd
man/zinbinom.Rd
src
src/R_interface.cpp
src/R_interface.h
src/densities.cpp
src/densities.h
src/init.cpp
src/logging.h
src/loghmm.cpp
src/loghmm.h
src/scalehmm.cpp
src/scalehmm.h
src/utility.cpp
src/utility.h
tests
tests/testthat
tests/testthat.R
tests/testthat/euploid_HB150318_1_003.bam_binsize_500000.RData
tests/testthat/test_convergence.R
tests/testthat/trisomy_BB150803_IV_003.bam_binsize_500000.RData
vignettes
vignettes/AneuFinder.Rnw
vignettes/references.bib
AneuFinder documentation built on May 20, 2017, 9:15 p.m.

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