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karyotapR
View on CRAN: Click
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Download and install karyotapR package within the R console
Install from CRAN:
install.packages("karyotapR")
Install from Github:
library("remotes")
install_github("cran/karyotapR") Install by package version:
library("remotes")
install_version("karyotapR", "1.0.2") Attach the package and use:
library("karyotapR")
Maintained by
Joseph Mays
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[Scholar Profile | Author Map]
All associated links for this package
First Published: 2023-09-07
Latest Update: 2023-09-07
Description:
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.
How to cite:
Joseph Mays (2023). karyotapR: DNA Copy Number Analysis for Genome-Wide Tapestri Panels. R package version 1.0.2, https://cran.r-project.org/web/packages/karyotapR. Accessed 14 Mar. 2026.
Previous versions and publish date:
1.0.1 (2023-09-07 10:50)
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Other R packages that karyotapR depends,
imports, suggests or enhances
Complete documentation for karyotapR
Functions, R codes and Examples using
the karyotapR R package
Some associated functions: PCAKneePlot . TapestriExperiment-class . assayBoxPlot . assayHeatmap . calcCopyNumber . calcGMMCopyNumber . calcNormCounts . calcSmoothCopyNumber . callSampleLables . corner . countBarcodedReads . createTapestriExperiment . getChrOrder . getCytobands . getGMMBoundaries . getTidyData . karyotapR-package . moveNonGenomeProbes . newTapestriExperimentExample . plotCopyNumberGMM . reducedDimPlot . runClustering . runPCA . runUMAP . slotGettersSetters .
Some associated R codes: GaussianMixtureCalls.R . clustering.R . copyNumberCalculation.R . createTapestriExperiment.R . getChrOrder.R . getCytobands.R . helperFunctions.R . karyotapR-package.R . moveNonGenomeProbes.R . normalization.R . parseBarcodedReads.R . plots.R . tapestriExperimentDefinition.R . Full karyotapR package functions and examples
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