In samuel-marsh/scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

---

all_times <- list()  # store the time for each chunk
knitr::knit_hooks$set(time_it = local({
  now <- NULL
  function(before, options) {
    if (before) {
      now <<- Sys.time()
    } else {
      res <- difftime(Sys.time(), now, units = "secs")
      all_times[[options$label]] <<- res
    }
  }
}))
knitr::opts_chunk$set(
  tidy = TRUE,
  tidy.opts = list(width.cutoff = 95),
  message = FALSE,
  warning = FALSE,
  time_it = TRUE
)

scCustomize requires R version 4.0 or greater. Highly recommend installing R Studio.

Install from CRAN

scCustomize can be installed from CRAN for all platforms using standard installation methods:

# Base R
install.packages("scCustomize")

# Using pak
pak::pkg_install("scCustomize")

Non-CRAN packages

A small number of functions in scCustomize rely on packages from Bioconductor and are not installed by default. To enable these functions make sure to install the following packages:

install.packages("BiocManager")

BiocManager::install(c("ComplexHeatmap", "dittoSeq", "DropletUtils", "Nebulosa"))

Optional CRAN packages

There are a few other CRAN packages that are needed to enable some optional functionality of scCustomize. To enable these functions make sure to install the following packages:

install.packages(c("ggpubr", "hdf5r", "rliger"))

Release Notes

A full copy of the changes in each version can be found in the NEWS/ChangeLog.

Develop branch

I also maintain a separate development branch^* that can be installed by supplying ref = "develop" in the devtools or remotes installation command. Version scheme vX.X.X.9yyy.

devtools::install_github(repo = "samuel-marsh/scCustomize", ref = "develop")

remotes::install_github(repo = "samuel-marsh/scCustomize", ref = "develop")

^*Note: While this branch is typically mostly stable it may contain breaking issues/bugs.
I do try and keep development ChangeLog up to date so it's easier to follow changes than reading commit history.

samuel-marsh/scCustomize documentation built on Dec. 20, 2024, 7:41 a.m.