R package for for single-cell RNA-seq clustering analysis.
if (!requireNamespace("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } install.packages( pkgs = "basejump", repos = c( "r.acidgenomics.com", BiocManager::repositories() ) )
pointillism currently supports these S4 single-cell container classes:
cell_data_set
Cell-cycle and cell-type markers are stored internally inside the package. Refer to inst/extdata/
for the source CSV files.
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()
.
The papers and software cited in our workflows are available as a shared library on Paperpile.