cardelino: clone identification from single-cell data 
cardelino contains a Bayesian method to infer clonal structure for a population of cells using single-cell RNA-seq data (and possibly other data modalities).
In its main mode cardelino requires:
-
An imperfect clonal tree structure inferred using, for example Canopy, from bulk or single-cell DNA sequencing data (e.g. bulk whole exome sequencing data).
-
Single-cell RNA sequencing data from which cell-specific somatic variants are called using, for example cellsnp-lite.
Installation
Release version
You can install the release version of cardelino from BioConductor:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("cardelino")Development version
The development version of cardelino can be installed using the
remotes package thus:
# install.packages("remotes")
remotes::install_github("single-cell-genetics/cardelino")Getting started
The best place to start are the vignettes. From inside an R session, load
cardelino and then browse the vignettes:
library(cardelino)
browseVignettes("cardelino")Notes on donor deconvolution
The donor demultiplex function, named Vireo, was previously supported in this R package, but now has been re-implemented in Python, which is more memory efficient and easier to run via a command line. We, therefore, highly recommend you switch to the Python version: https://vireoSNP.readthedocs.io.
The vireo function is not supported from version >=0.5.0. If you want to use the R functions, please use the version ==0.4.2 or lower. You can also find it in a separate branch in this repository: with_vireo branch or use the donor_id.R file directly. However, using the Python implementation of Vireo is strongly recommended.
Code of Conduct
Please note that the cardelino project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
Citation
If you find cardelino helpful please consider citing:
McCarthy, D.J., Rostom, R., Huang, Y. et al. (2020) Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes. Nature Methods
About the name
cardelino is almost an anagram of "clone ID R" and is almost the same as the
Italian for "goldfinch", a common and attractive European bird, pictured below
and used in cardelino's hex sticker. In the Western art canon, the goldfinch
is considered a "saviour" bird
and appears in notable paintings from the Italian renaissance
and the Dutch Golden Age.
Perhaps this package may prove a saviour for certain single-cell datasets!
Acknowledgement:
The cardelino image was produced by Darren Bellerby. It was obtained from
Flickr
and is reproduced here under a CC-BY-2.0
licence.