Infer Ploidy of Single Cells.
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')