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.
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"))
In order to install the most recent 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')