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

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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("AneuFinder")
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
Version1.2.1
https://github.com/ataudt/aneufinder.git

View on Bioconductor

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

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

correctGC: GC correction

correctMappability: Mappability correction

deltaWCalculator: Calculate deltaWs

DNAcopy.findCNVs: Find copy number variations (DNAcopy)

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)

fixedWidthBins: Make fixed-width bins

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

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

plotProfile: Read count and CNV profile

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

aneuBiHMM Man page
Aneufinder Man page
AneuFinder Man page
AneuFinder-package Man page
aneuHMM Man page
bam2GRanges Man page
bed2GRanges Man page
binned.data Man page
binning Man page
binReads Man page
bivariate.findCNVs Man page
blacklist Man page
clusterByQuality Man page
collapseBins Man page
colors Man page
compareMethods Man page
compareModels Man page
correctGC Man page
correctMappability Man page
deltaWCalculator Man page
DNAcopy.findCNVs Man page
dzinbinom Man page
estimateComplexity Man page
export Man page
exportCNVs Man page
exportGRanges Man page
exportReadCounts Man page
filterSegments Man page
findCNVs Man page
findCNVs.strandseq Man page
fixedWidthBins Man page
getQC Man page
getSCEcoordinates Man page
getSegments Man page
heatmapAneuploidies Man page
heatmapGenomewide Man page
hotspotter Man page
importBed Man page
initializeStates Man page
karyotypeMeasures Man page
loadFromFiles Man page
plot.aneuBiHMM Man page
plot.aneuHMM Man page
plot.character Man page
plot.GRanges Man page
plotHeterogeneity Man page
plotHistogram Man page
plotKaryogram Man page
plotProfile Man page
pzinbinom Man page
qc.bhattacharyya Man page
qc.entropy Man page
qc.sos Man page
qc.spikiness Man page
qualityControl Man page
qzinbinom Man page
readConfig Man page
rzinbinom Man page
simulateReads Man page
stateColors Man page
strandColors Man page
subsetByCNVprofile Man page
transCoord Man page
univariate.findCNVs Man page
variableWidthBins Man page
writeConfig Man page
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/correctionMethods.R R/deltaWCalculator.R R/dnbinom.R R/documented_objects.R R/export.R R/findCNVs.R R/findSCEs.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/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/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/correctGC.Rd man/correctMappability.Rd man/deltaWCalculator.Rd man/estimateComplexity.Rd man/export.Rd man/filterSegments.Rd man/findCNVs.Rd man/findCNVs.strandseq.Rd man/fixedWidthBins.Rd man/getQC.Rd man/getSCEcoordinates.Rd man/getSegments.Rd man/heatmapAneuploidies.Rd man/heatmapGenomewide.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/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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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