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.