scPloidy

scPloidy is an R package to compute ploidy of single cells (or nuclei) based on single-cell (or single-nucleus) ATAC-seq data. In ATAC-seq, open chromatin regions are excised and sequenced. For any site on the genome, ATAC-seq could read 0, 1 or 2 DNA fragments, if the cell was diploid. If the cell was tetraploid, ATAC-seq could read 0, 1, 2, 3 or 4 fragments from the same site. This is the basic idea used in scPloidy. We model the depth of DNA sequencing at one site by binomial distribution.

Manuscript available in bioRxiv.

Questions? Please submit to GitHub Issues or e-mail fumihiko AT takeuchi DOT name

Installation in R

Beforehand, these packages need to be installed from Bioconductor:

if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install(c("GenomicRanges", "IRanges", "Rsamtools"))

Install from CRAN:

install.packages('scPloidy')

In order to install the developmental version:

install.packages('devtools')
devtools::install_github('fumi-github/scPloidy', build_vignettes = TRUE)

To uninstall package:

remove.packages('scPloidy')

Usage

library(scPloidy)
vignette('intro', package = 'scPloidy')