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


R method

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    pkgs = "basejump",
    repos = c(

Supported data classes

pointillism currently supports these S4 single-cell container classes:


Cell-cycle and cell-type markers are stored internally inside the package. Refer to inst/extdata/ for the source CSV files.


Maximal number of DLLs reached

Error: package or namespace load failed for 'pointillism' 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:


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().


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