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.
Additionally, this method can be adapted to detect the proliferating stage in the cell cycle and copy number variations in cancer cells.
The algorithm should also work for single-cell (or single-nucleus) whole genome sequencing, if the template DNA is tagmented first. It does not work for whole genome amplified DNA.
This is published in Genetics. Related data is available from figshare.
scPloidy can also be used for detecting multiplets (doublets, triplets) in single-cell assay. Based on biological knowledge, if the cells in your sample are likely all diploids, you can regard the detected polyploid cells as multiplets. Indeed, scPloidy can detect aggregation of cells of the same cell type, which cannot be detected by RNA-seq based algorithms (e.g., Scrublet, DoubletFinder, DoubletDecon).
Questions? Please submit to GitHub Issues or e-mail fumihiko AT takeuchi DOT name
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')
library(scPloidy)
vignette('intro', package = 'scPloidy')