R package for for single-cell RNA-seq clustering analysis.

Installation

This is an R package.

Bioconductor

We recommend installing the package with BiocManager.

if (!require("BiocManager")) {
    install.packages("BiocManager")
}
BiocManager::install(
    pkgs = c(
        "devtools",
        "remotes",
        "GenomeInfoDbData"
    )
)
BiocManager::install(
    pkgs = "steinbaugh/pointillism",
    dependencies = c("Depends", "Imports", "Suggests")
)

For R < 3.5, BiocManager is not supported. Use BiocInstaller::biocLite() instead of BiocManager::install(). This requires sourcing the legacy Bioconductor biocLite.R script.

# try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")

Markers

Shared cell-cycle markers and cell-type markers are available on Google Sheets. Contact Michael Steinbaugh if you’d like to contribute to this list, and he’ll enable write access.

Troubleshooting

Maximal number of DLLs reached

Error: package or namespace load failed for 'bcbioSingleCell' in dyn.load(file, DLLpath = DLLpath, ...):
  maximal number of DLLs reached...

Depending on your operating system, you may encounter this error about hitting the DLL limit in R. This issue is becoming more common as RNA-seq analysis packages grow increasingly complex. Luckily, we can configure R to increase the DLL limit. Append this line to your ~/.Renviron file:

R_MAX_NUM_DLLS=150

For more information on this issue, consult help("dyn.load") in the R documentation. The number of loaded DLLs in an R session can be obtained with getLoadedDLLs().

References

The papers and software cited in our workflows are available as a shared library on Paperpile.