karyotapR

karyotapR enables analysis of DNA copy number (aneuploidy) using data produced by the KaryoTap method. 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.

KaryoTap combines custom genome-wide targeted DNA sequencing panels for the Mission Bio Tapestri system with a Gaussian mixture model framework for calling copy number.

References

Mays JC et al., 2023. KaryoTap Enables Aneuploidy Detection in Thousands of Single Human Cells. https://www.biorxiv.org/content/10.1101/2023.09.08.555746v1.

Installation

You can install the current stable version of karyotapR from CRAN with:

install.packages('karyotapR')

You can install the development version of karyotapR from GitHub with:

# install.packages("devtools")
devtools::install_github("joeymays/karyotapR")

Workflow

For details on the workflow, see the Getting Started guide, articles on this site, and the package reference/documentation.