Package: AneuFinder 1.35.1
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:
AneuFinder_1.35.1.tar.gz
AneuFinder_1.35.1.zip(r-4.4)AneuFinder_1.35.1.zip(r-4.3)
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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')) |
Bug tracker:https://github.com/ataudt/aneufinder/issues
On BioConductor:AneuFinder-1.35.0(bioc 3.21)AneuFinder-1.34.0(bioc 3.20)
immunooncologysoftwaresequencingsinglecellcopynumbervariationgenomicvariationhiddenmarkovmodelwholegenomecpp
Last updated 3 days agofrom:c4b7a76670. Checks:1 OK, 3 NOTE, 2 WARNING. Indexed: yes.
Target | Result | Latest binary |
---|---|---|
Doc / Vignettes | OK | Mar 27 2025 |
R-4.4-win-x86_64 | NOTE | Mar 27 2025 |
R-4.4-mac-x86_64 | NOTE | Mar 27 2025 |
R-4.4-linux-x86_64 | NOTE | Mar 27 2025 |
R-4.3-win-x86_64 | WARNING | Mar 27 2025 |
R-4.3-mac-x86_64 | WARNING | Mar 27 2025 |
Exports:Aneufinderbam2GRangesbed2GRangesbinReadsblacklistbreakpointColorsclusterByQualityclusterHMMscollapseBinscompareMethodsconsensusSegmentscorrectGCexportCNVsexportGRangesexportReadCountsfilterSegmentsfindCNVsfindCNVs.strandseqfindHotspotsfixedWidthBinsgetBreakpointsgetQCgetSCEcoordinatesheatmapAneuploidiesheatmapGenomewideheatmapGenomewideClustersimportBedkaryotypeMeasuresloadFromFilesplot_pcaplotHeterogeneityrefineBreakpointssimulateReadsstateColorsstrandColorssubsetByCNVprofilevariableWidthBins
Dependencies:abindAneuFinderDataaskpassbamsignalsBHBiobaseBiocGenericsBiocParallelBiostringsbitopsclicodetoolscolorspacecowplotcpp11crayoncurlDelayedArrayDNAcopydoParallelecpfansifarverforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggdendroggplot2ggrepelgluegtablehttrIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmgcvmimemunsellnlmeopensslpillarpkgconfigplyrR6RColorBrewerRcppreshape2RhtslibrlangRsamtoolsS4ArraysS4VectorsscalessnowSparseArraystringistringrSummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc