Package: karyotapR 1.0.1.9000

karyotapR: DNA Copy Number Analysis for Genome-Wide Tapestri Panels
Analysis of DNA copy number in single cells using custom genome-wide targeted DNA sequencing panels for the Mission Bio Tapestri platform. Users can easily parse, manipulate, and visualize datasets produced from the automated 'Tapestri Pipeline', with support for normalization, clustering, and copy number calling. Functions are also available to deconvolute multiplexed samples by genotype and parsing barcoded reads from exogenous lentiviral constructs.
Authors:
karyotapR_1.0.1.9000.tar.gz
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karyotapR.pdf |karyotapR.html✨
karyotapR/json (API)
NEWS
# Install 'karyotapR' in R: |
install.packages('karyotapR', repos = c('https://joeymays.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/joeymays/karyotapr/issues
Pkgdown site:https://joeymays.xyz
Last updated 1 years agofrom:f675f908c0. Checks:4 OK, 5 NOTE. Indexed: yes.
Target | Result | Latest binary |
---|---|---|
Doc / Vignettes | OK | Mar 08 2025 |
R-4.5-win | NOTE | Mar 08 2025 |
R-4.5-mac | NOTE | Mar 08 2025 |
R-4.5-linux | NOTE | Mar 08 2025 |
R-4.4-win | OK | Mar 08 2025 |
R-4.4-mac | OK | Mar 08 2025 |
R-4.4-linux | OK | Mar 08 2025 |
R-4.3-win | NOTE | Mar 08 2025 |
R-4.3-mac | NOTE | Mar 08 2025 |
Exports:.TapestriExperimentassayBoxPlotassayHeatmapbarcodeProbebarcodeProbe<-calcCopyNumbercalcGMMCopyNumbercalcNormCountscalcSmoothCopyNumbercallSampleLablescornercountBarcodedReadscountBarcodedReadsFromContigcreateTapestriExperimentgenerateControlCopyNumberTemplategetChrOrdergetCytobandsgetGMMBoundariesgetTidyDatagmmParamsgrnaProbegrnaProbe<-moveNonGenomeProbesnewTapestriExperimentExamplePCAKneePlotplotCopyNumberGMMreducedDimPlotrunClusteringrunPCArunUMAPshow
Dependencies:abindaskpassBiobaseBiocGenericscirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurldbscanDelayedArraydigestdoParalleldplyrfansifarverfitdistrplusforeachgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggplot2GlobalOptionsgluegtablegtoolsherehttrIRangesisobanditeratorsjsonlitelabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigpngpurrrR6rappdirsRColorBrewerRcppRcppEigenRcppTOMLreticulaterhdf5rhdf5filtersRhdf5librjsonrlangrprojrootRSpectraS4ArraysS4VectorsscalesshapeSingleCellExperimentSparseArraystringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectUCSC.utilsumaputf8vctrsviridisLitewithrXVector