This R package contains two major methods to analysis single-cell RNA-seq data

• cardelino to reconstructing somatic clonal tree and assigning single cells to clones. See cardelino munual
• Vireo to demultiplex pooled scRNA-seq with or without genotype reference. See Vireo manual or run our wrap run_vireo.R in a command line with Rscript:

  Rscript run_vireo.R $CELL_FILE $OUT_DIR $N_DONOR [$GT_VCF_FILE]
  

Note: Vireo is now re-implemented in Python, which is more memory efficient and easier to run via a command line. We may turn off Vireo in R but mainly maintain the Python in future, so please consider switch: https://vireoSNP.readthedocs.io

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

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

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.

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.

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.

Vireo(variational inference for reconstructing ensemebl origin) is a Latin word referring to a green migratory bird, perhaps the female golden oriole, possibly the European greenfinch

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.