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.

AuthorAaron Taudt, Bjorn Bakker, David Porubsky
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

Files in this package

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

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