README.md

In steinbaugh/pointillism: Single-cell RNA-seq toolkit

pointillism

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

Installation

R method

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}
install.packages(
    pkgs = "pointillism",
    repos = c(
        "https://r.acidgenomics.com",
        BiocManager::repositories()
    ),
    dependencies = TRUE
)

Supported data classes

pointillism currently supports these S4 single-cell container classes:

• SingleCellExperiment
• Seurat
• monocle3 cell_data_set

Markers

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

Troubleshooting

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:

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.

steinbaugh/pointillism documentation built on Oct. 13, 2023, 10:43 p.m.