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.

Author
Aaron Taudt, Bjorn Bakker, David Porubsky
Date of publication
None
Maintainer
Aaron Taudt <aaron.taudt@gmail.com>
License
Artistic-2.0
Version
1.2.0
URLs

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