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/\u003e\n\n\u003c!-- badges: start --\u003e\n[![R build status](https://github.com/single-cell-genetics/cardelino/workflows/R-CMD-check/badge.svg)](https://github.com/single-cell-genetics/cardelino/actions)\n\u003c!-- badges: end --\u003e\n\n**cardelino** contains a Bayesian method to infer clonal structure for a \npopulation of cells using single-cell RNA-seq data (and possibly other data \nmodalities). \n\nIn its main mode **cardelino** requires: \n\n* An imperfect clonal tree structure inferred using, for example [Canopy](https://cran.r-project.org/web/packages/Canopy/index.html), from bulk or single-cell DNA sequencing data (e.g. bulk whole exome sequencing data).\n\n* Single-cell RNA sequencing data from which cell-specific somatic variants are called using, for example [cellsnp-lite](https://github.com/single-cell-genetics/cellsnp-lite).\n\n## Installation\n\n### Release version\n\nYou can install the release version of `cardelino` from BioConductor:\n\n```r\nif (!requireNamespace(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\n\nBiocManager::install(\"cardelino\")\n```\n\n### Development version\n\nThe development version of `cardelino` can be installed using the \n[`remotes`](https://remotes.r-lib.org/) package thus:\n\n```r\n# install.packages(\"remotes\")\nremotes::install_github(\"single-cell-genetics/cardelino\")\n```\n\n## Getting started\n\nThe best place to start are the vignettes. From inside an R session, load \n`cardelino` and then browse the vignettes:\n\n```r\nlibrary(cardelino)\nbrowseVignettes(\"cardelino\")\n```\n\n## Notes on donor deconvolution\n\nThe donor demultiplex function, named Vireo, was previously supported in this \nR package, but now has been re-implemented in Python, which is more memory \nefficient and easier to run via a command line. We, therefore, highly recommend \nyou switch to the Python version: https://vireoSNP.readthedocs.io. \n\nThe vireo function is not supported from version \u003e=0.5.0. If you want to use the\nR functions, please use the version ==0.4.2 or lower. You can also find it in a\nseparate branch in this repository: [with_vireo branch](https://github.com/single-cell-genetics/cardelino/tree/with_vireo)\nor use the [donor_id.R](https://github.com/single-cell-genetics/cardelino/blob/with_vireo/R/donor_id.R) \nfile directly. However, using the Python implementation of Vireo is **strongly** recommended. \n\n## Code of Conduct\n\nPlease note that the cardelino project is released with a [Contributor Code of Conduct](http://bioconductor.org/about/code-of-conduct/).\nBy contributing to this project, you agree to abide by its terms.\n\n## Citation\n\nIf you find cardelino helpful please consider citing: \n\n\u003e McCarthy, D.J., Rostom, R., Huang, Y. et al. (2020)\n\u003e Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes.\n\u003e Nature Methods\n\n## About the name\n\n`cardelino` is almost an anagram of \"clone ID R\" and is almost the same as the \nItalian for \"goldfinch\", a common and attractive European bird, pictured below\nand used in `cardelino`'s hex sticker. In the Western art canon, the goldfinch \nis considered a [\"saviour\" bird](https://en.wikipedia.org/wiki/European_goldfinch) \nand appears in notable paintings from the [Italian renaissance](https://en.wikipedia.org/wiki/Madonna_del_cardellino)\nand the [Dutch Golden Age](https://en.wikipedia.org/wiki/The_Goldfinch_(painting)). \nPerhaps this package may prove a saviour for certain single-cell datasets!\n\n\u003cimg src=inst/cardelino_med.jpg height=\"200\"\u003e\n\n**Acknowledgement:**\nThe `cardelino` image was produced by [Darren Bellerby](https://www.flickr.com/photos/world-birds/). It was obtained from\n[Flickr](https://www.flickr.com/photos/world-birds/18740373165/in/photolist-uy2j3a-uxAdib-aLcHGB-9BjDvc-YkgQg7-QN9Tr1-BVjkHh-8oWiKC-WFkDcS-nhZzXt-Y4zM2h-zULNgX-7uZCFT-f5ghc4-Ugx9pj-UJ5tog-7v4rVy-7wsLpm-bru3Ha-JnmcUQ-frkUqa-bohcgU-KAB14-dieCGY-FJ6n6A-GHJ5UK-X2qjGh-8cAjtw-FshfBi-8cwZst-qEMHSX-dTtAUs-EtqKxo-oZdJB3-8cx1Tn-D1jHjU-PWzWY2-brtKfH-ch2tvW-qEFKTd-wVmxsG-oYZbhP-Aa5cBB-h6aQf6-9Bny23-ayfnFS-dgG2Kn-QUyKgf-bBc31B-cVik3)\nand is reproduced here under a CC-BY-2.0\n[licence](https://creativecommons.org/licenses/by/2.0/legalcode).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsingle-cell-genetics%2Fcardelino","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsingle-cell-genetics%2Fcardelino","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsingle-cell-genetics%2Fcardelino/lists"}