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Installing Cellucid for R

Source: vignettes/installation.Rmd
installation.Rmd

Current version and availability

The active Cellucid for R source and documentation version is 0.9.7. It is the CRAN submission release. The CRAN package index is authoritative for registry availability. Use the CRAN command below when the index lists cellucid 0.9.7; otherwise use the GitHub command.

Requirements

  • R 4.1.0 or newer
  • An internet connection while installing the package
  • The remotes package only when installation from GitHub is needed

Cellucid compiles a few small C routines (the CRC-32 checksum of the .zarr.zip writer, the SHA-256 that checks the downloaded web app, the latent-space outlier quantiles, one-pass checks of large matrices, and the decoders of a saved session, linked against zlib). Installing from source needs Rtools on Windows, the Xcode Command Line Tools on macOS, or a C toolchain plus the R and zlib development headers on Linux (for example r-base-dev, which brings zlib1g-dev, on Debian and Ubuntu). A platform CRAN binary, when available, does not require a local compiler. The viewer (cellucid_view(), cellucid_serve()) uses httpuv, later and curl, which are installed with the package. The optional Matrix package is recommended for sparse expression matrices and neighbour graphs; SeuratObject and SingleCellExperiment (with SummarizedExperiment) are needed only to read their own objects.

Check your R version with:

R.version.string

Install version 0.9.7 from CRAN

When the CRAN package index lists cellucid 0.9.7, install it with: 

install.packages("cellucid")

If the index does not list version 0.9.7 yet, install the active source from the official GitHub repository:

install.packages("remotes")
remotes::install_github("theislab/cellucid-r")

Install the recommended sparse-matrix support when your data uses sparse expression or connectivity matrices:

On R older than 4.4, CRAN’s current Matrix release does not install, and SeuratObject 5 needs Matrix 1.6-4 or later. Install Matrix 1.6-5, the last release for those R versions, before SeuratObject:

remotes::install_version("Matrix", version = "1.6-5")

Restart R after upgrading an installation that was already loaded in the current session.

Update an existing installation

Install again from the source currently available to you. Use CRAN when its package index lists version 0.9.7: 

install.packages("cellucid")

Otherwise update directly from the official source repository:

remotes::install_github("theislab/cellucid-r")

Restart R after the update so the current session does not retain the package version that was loaded earlier.

Verify the installation

Load Cellucid and confirm that R reports the active version:

library(cellucid)
packageVersion("cellucid")
#> [1] '0.9.7'

You can then open the preparation function reference:

?cellucid_prepare

Continue with Preparing data for Cellucid for a complete example, or use the R package guide for Seurat and SingleCellExperiment recipes.

Next step

Once the package is installed, write a Cellucid-ready AnnData store with cellucid_prepare() and open it in the Cellucid web app. The function reference documents every input and validation rule.