shians/cardelino

cardelino: clone and donor identification from single-cell data

This R package contains methods to assign donor and clone identities to individual cells from single-cell RNA-sequencing data.

Installation

From R

The cardelino package can be conveniently installed using the devtools package thus:

devtools::install_github("PMBio/cardelino", build_vignettes = TRUE)

Cardelino in a container

For situations in which installing software is a challenge (for example, on institutional HPC clusters or on cloud computing platforms), we provide a pre-built Docker image on DockerHub. This image contains R version 3.5.0 with cardelino and other packages (e.g. tidyverse, basic Bioconductor and other single-cell RNA-seq packages) installed and ready to use with Docker or Singularity.

For example, to build a Singularity image that can be used on an HPC cluster (with Singularity installed) one simply pulls the image from DockerHub:

singularity build rsc.img docker://davismcc/r-singlecell-img

This builds a Singularity image called rsc.img in the current working directory. We can then run R from the container and use the installed version of cardelino:

singularity exec rsc.img R

Equivalent commands enable running R from the container with Docker.

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")

Vignettes for the donor identification and clone identification use cases are provided.

Accessing the vignettes from within your R session is recommended, but you can also view the clone ID vignette and view the donor ID vignette online.

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. 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.