Package: AneuFinder 1.33.0

Aaron Taudt

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

AneuFinder implements functions for copy-number detection, breakpoint detection, and karyotype and heterogeneity analysis in single-cell whole genome sequencing and strand-seq data.

Authors:Aaron Taudt, Bjorn Bakker, David Porubsky

AneuFinder_1.33.0.tar.gz
AneuFinder_1.33.0.zip(r-4.5)AneuFinder_1.33.0.zip(r-4.4)AneuFinder_1.33.0.zip(r-4.3)
AneuFinder_1.33.0.tgz(r-4.4-arm64)AneuFinder_1.33.0.tgz(r-4.4-x86_64)AneuFinder_1.33.0.tgz(r-4.3-arm64)AneuFinder_1.33.0.tgz(r-4.3-x86_64)
AneuFinder_1.33.0.tar.gz(r-4.5-noble)AneuFinder_1.33.0.tar.gz(r-4.4-noble)
AneuFinder_1.33.0.tgz(r-4.4-emscripten)AneuFinder_1.33.0.tgz(r-4.3-emscripten)
AneuFinder.pdf |AneuFinder.html✨
AneuFinder/json (API)
NEWS

# Install 'AneuFinder' in R:
install.packages('AneuFinder', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ataudt/aneufinder/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:AneuFinder-1.33.0(bioc 3.20)AneuFinder-1.32.0(bioc 3.19)

bioconductor-package

37 exports 3.14 score 83 dependencies 16 mentions

Last updated 2 months agofrom:0fb90c6e77

Exports:Aneufinderbam2GRangesbed2GRangesbinReadsblacklistbreakpointColorsclusterByQualityclusterHMMscollapseBinscompareMethodsconsensusSegmentscorrectGCexportCNVsexportGRangesexportReadCountsfilterSegmentsfindCNVsfindCNVs.strandseqfindHotspotsfixedWidthBinsgetBreakpointsgetQCgetSCEcoordinatesheatmapAneuploidiesheatmapGenomewideheatmapGenomewideClustersimportBedkaryotypeMeasuresloadFromFilesplot_pcaplotHeterogeneityrefineBreakpointssimulateReadsstateColorsstrandColorssubsetByCNVprofilevariableWidthBins

Dependencies:abindAneuFinderDataaskpassbamsignalsBHBiobaseBiocGenericsBiocParallelBiostringsbitopsclicodetoolscolorspacecowplotcpp11crayoncurlDelayedArrayDNAcopydoParallelecpfansifarverforeachformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggdendroggplot2ggrepelgluegtablehttrIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmgcvmimemunsellnlmeopensslpillarpkgconfigplyrR6RColorBrewerRcppreshape2RhtslibrlangRsamtoolsS4ArraysS4VectorsscalessnowSparseArraystringistringrSummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

A quick introduction to AneuFinder

Rendered fromAneuFinder.Rnwusingknitr::knitron Jul 05 2024.

Last update: 2020-03-17
Started: 2016-03-07

Readme and manuals

Help Manual

Help pageTopics
Copy-number detection in WGSCS and Strand-Seq dataAneuFinder-package AneuFinder
Bivariate Hidden Markov ModelaneuBiHMM
Wrapper function for the 'AneuFinder' packageAneufinder
Hidden Markov ModelaneuHMM
Annotate breakpointsannotateBreakpoints
Import BAM file into GRangesbam2GRanges
Import BED file into GRangesbed2GRanges
Find copy number variations (edivisive, bivariate)bi.edivisive.findCNVs
Find copy number variations (DNAcopy, bivariate)biDNAcopy.findCNVs
Find copy number variations (bivariate)biHMM.findCNVs
Binned read countsbinned.data
Bin the genomebinning
Convert aligned reads from various file formats into read counts in equidistant binsbinReads
Make a blacklist for genomic regionsblacklist
Cluster based on quality variablesclusterByQuality
Cluster objectsclusterHMMs
Collapse consecutive binscollapseBins
'AneuFinder' color schemebreakpointColors colors stateColors strandColors
Compare copy number calling methodscompareMethods
Compare copy number modelscompareModels
Make consensus segmentsconsensusSegments
GC correctioncorrectGC
Find copy number variations (DNAcopy, univariate)DNAcopy.findCNVs
Find copy number variations (edivisive, univariate)edivisive.findCNVs
Estimate library complexityestimateComplexity
Export genome browser viewable filesexport exportCNVs exportGRanges exportReadCounts
Filter segments by minimal sizefilterSegments
Find copy number variationsfindCNVs
Find copy number variations (strandseq)findCNVs.strandseq
Find breakpoint hotspotsfindHotspots
Make fixed-width binsfixedWidthBins
Extract breakpointsgetBreakpoints
Get distinct colorsgetDistinctColors
Obtain a data.frame with quality metricsgetQC
Get SCE coordinatesgetSCEcoordinates
Plot aneuploidy stateheatmapAneuploidies
Genome wide heatmap of CNV-stateheatmapGenomewide
Plot heatmaps for quality controlheatmapGenomewideClusters
Find copy number variations (univariate)HMM.findCNVs
Find hotspots of genomic eventshotspotter
Find hotspots of genomic eventshotspotter.variable
Read bed-file into GRangesimportBed
Initialize state factor levels and distributionsinitializeStates
Measures for Karyotype HeterogeneitykaryotypeMeasures
Load 'AneuFinder' objects from fileloadFromFiles
Merge Strand-seq librariesmergeStrandseqFiles
Perform a PCA for copy number profilesplot_pca
Plotting function for 'aneuBiHMM' objectsplot.aneuBiHMM
Plotting function for 'aneuHMM' objectsplot.aneuHMM
Plotting function for saved 'AneuFinder' objectsplot.character
Plotting function for binned read countsplot.GRanges
Plotting function for binned read counts (list)plot.GRangesList
Heterogeneity vs. AneuploidyplotHeterogeneity
Plot a histogram of binned read counts with fitted mixture distributionplotHistogram
Karyogram-like chromosome overviewplotKaryogram
Read count and CNV profileplotProfile
Print aneuBiHMM objectprint.aneuBiHMM
Print aneuHMM objectprint.aneuHMM
Quality control measures for binned read countsqc.bhattacharyya qc.entropy qc.sos qc.spikiness qualityControl
Read AneuFinder configuration filereadConfig
Refine breakpointsrefineBreakpoints
Simulate reads from genomesimulateReads
Get IDs of a subset of modelssubsetByCNVprofile
Transform genomic coordinatestransCoord
Make variable-width binsvariableWidthBins
Write AneuFinder configuration filewriteConfig
The Zero-inflated Negative Binomial Distributiondzinbinom pzinbinom qzinbinom rzinbinom zinbinom