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# cardelino: clone identification from single-cell data <img src="inst/cardelino_sticker.png" align="right" width="160" /> <!-- badges: start --> [![R build status](]( <!-- badges: end --> **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: ```r 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: ```r # 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: ```r 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: 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! <img src=inst/cardelino_med.jpg height="200"> **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](