Environment Load and Check

• this code section is packaged as an include for reuse across all examples
• it uses the HTML details tag directly to wrap code blocks and output as drop-down sections

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library(patchwork)
library(dplyr)

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

library(Seurat)

Loading required package: SeuratObject

Loading required package: sp

'SeuratObject' was built under R 4.3.0 but the current version is
4.3.2; it is recomended that you reinstall 'SeuratObject' as the ABI
for R may have changed

Attaching package: 'SeuratObject'

The following object is masked from 'package:base':

    intersect

• Is there a typo in the message above? Application Programming Interface, API != ABI

• Rolling back to R 4.3.0 was not possible with the current version of Seurat

  • the indication was that Seurat requires a version of base Matrix that is not present in R 4.3.0

# which Seurat?
packageVersion("Seurat")

[1] '5.0.0'

# which R?
version[['version.string']]

[1] "R version 4.3.2 (2023-10-31)"

# presto was installed 
# For a (much!) faster implementation of the 
# Wilcoxon Rank Sum Test
packageVersion('presto')

[1] '1.0.0'

# check python is available via reticulate
import sys
print(sys.version.split(" ")[0])

3.12.0

# shell check
python3 -V

Python 3.12.0

# shell check
quarto -v

1.4.489

Functions

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# Useful for code development.
# Save the object at a point and reload it into the R console 
# i.e. for developing alternative reports 
# without having to run the pipeline right from the start
# which can be slow
#
# NB: Files produced by saveRDS (or serialized to a file connection) 
# are not suitable as an interchange format between machines
# 
# For that use hdf5 or transfer data and code to reproduce the result 

saveRDS_overwrite <- function(file_path) {
  if (file.exists(file_path)) {
    file.remove(file_path)
  } 
  saveRDS(pbmc, file = file_path)
}