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.

Version: 1.0.1
Depends: R (≥ 3.6), SingleCellExperiment
Imports: circlize, cli, ComplexHeatmap, dbscan, dplyr, fitdistrplus, GenomicRanges, ggplot2, gtools, IRanges, magrittr, methods, purrr, rhdf5, rlang, S4Vectors, stats, SummarizedExperiment, tibble, tidyr, umap, viridisLite
Suggests: Biostrings, knitr, rmarkdown, Rsamtools, testthat (≥ 3.0.0)
Published: 2023-09-07
Author: Joseph Mays ORCID iD [aut, cre, cph]
Maintainer: Joseph Mays <josephcmays at gmail.com>
BugReports: https://github.com/joeymays/karyotapR/issues
License: MIT + file LICENSE
URL: https://github.com/joeymays/karyotapR, http://joeymays.xyz/karyotapR/
NeedsCompilation: no
Materials: README NEWS
CRAN checks: karyotapR results

Documentation:

Reference manual: karyotapR.pdf

Downloads:

Package source: karyotapR_1.0.1.tar.gz
Windows binaries: r-devel: karyotapR_1.0.1.zip, r-release: karyotapR_1.0.1.zip, r-oldrel: karyotapR_1.0.1.zip
macOS binaries: r-release (arm64): not available, r-oldrel (arm64): karyotapR_1.0.1.tgz, r-release (x86_64): not available

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