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("remotes")
BiocManager::install("steinbaugh/pointillism")

Supported data classes

pointillism currently supports these S4 single-cell container classes:

Seurat v3: The current release of pointillism is compatible only with Seurat v2. The forthcoming v3 update introduces many code-breaking changes to the Seurat class structure. I’ll release an update to pointillism that supports Seurat v3 when it becomes available on CRAN.

monocle v3: Support for the monocle CellDataSet class will be added when monocle v3 becomes available on Bioconductor.

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.

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.