Change R Dependencies

api/r/cellxgene.census/DESCRIPTION

@@ -21,15 +21,15 @@ Imports:
   httr,
   jsonlite,
   methods,
-  Seurat (>= 4.1.0),
-  SingleCellExperiment (>= 1.20.0),
   stats,
   tiledbsoma,
   tiledb
 Suggests:
   bit64,
   knitr,
   rmarkdown,
+  SingleCellExperiment (>= 1.20.0),
+  Seurat (>= 4.1.0),
   testthat (>= 3.0.0),
   withr
 Config/testthat/edition: 3

api/r/cellxgene.census/R/get_helpers.R

@@ -69,6 +69,10 @@ get_seurat <- function(
     var_coords = NULL,
     var_column_names = NULL,
     var_index = "feature_id") {
+  stopifnot(
+    "R package 'Seurat' is not installed." = require("Seurat", quietly = T)
+  )
+
   expt_query <- tiledbsoma::SOMAExperimentAxisQuery$new(
     get_experiment(census, organism),
     measurement_name,
@@ -135,6 +139,10 @@ get_single_cell_experiment <- function(
     var_coords = NULL,
     var_column_names = NULL,
     var_index = "feature_id") {
+  stopifnot(
+    "R package 'SingleCellExperiment' is not installed." = require("SingleCellExperiment", quietly = T)
+  )
+
   expt_query <- tiledbsoma::SOMAExperimentAxisQuery$new(
     get_experiment(census, organism),
     measurement_name,

api/r/cellxgene.census/README.md

@@ -12,11 +12,13 @@ Census data can be fetched in an iterative fashion for bigger-than-memory slices
 
 ## Installation
 
-From an R session, first install `tiledb` from R-Universe, the latest release in CRAN is not yet available.
+If installing from **Ubuntu**, you may need to install the following libraries via `apt install`,  `libxml2-dev` `libssl-dev` `libcurl4-openssl-dev`. In addition you must have `camke` v3.21 or greater.
+
+If installing from **MacOS**, you will need to install the [developer tools `Xcode`](https://apps.apple.com/us/app/xcode/id497799835?mt=12).
 
-If installing from Ubuntu, you may need to install the following libraries via `apt install`:  `libxml2-dev` `libssl-dev` `libcurl4-openssl-dev`.
+**Windows** is not supported.
 
-If installing from MacOS, you will need to install the [developer tools `Xcode`](https://apps.apple.com/us/app/xcode/id497799835?mt=12).
+From an R session, first install `tiledb` from R-Universe, the latest release in CRAN is not yet available.
 
 ```r
 install.packages(
@@ -26,7 +28,7 @@ install.packages(
 )
 ```
 
-Then install `cellxgene.census` from R-Universe.
+Then in an R session install `cellxgene.census` from R-Universe.
 
 ```r
 install.packages(
@@ -35,6 +37,20 @@ install.packages(
 )
 ```
 
+To be able to export Census data to `Seurat` or `SingleCellExperiment` you also need to install their respective packages.
+
+```r
+# Seurat
+install.packages("Seurat")
+
+# SingleCellExperiment
+if (!require("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+
+BiocManager::install("SingleCellExperiment")
+```
+
+
 ## Usage
 
 Check out the vignettes in the "Articles" section of the navigation bar on this site. We highly recommend the following vignettes as a starting point:

docs/cellxgene_census_docsite_installation.md

@@ -29,11 +29,13 @@ If installing in a Databricks notebook environment, use `%pip install`. Do not u
 
 ## R
 
-From an R session, first install `tiledb` from R-Universe, the latest release in CRAN is not yet available.
+If installing from **Ubuntu**, you may need to install the following libraries via `apt install`,  `libxml2-dev` `libssl-dev` `libcurl4-openssl-dev`. In addition you must have `camke` v3.21 or greater.
+
+If installing from **MacOS**, you will need to install the [developer tools `Xcode`](https://apps.apple.com/us/app/xcode/id497799835?mt=12).
 
-If installing from Ubuntu, you may need to install the following libraries via `apt install`:  `libxml2-dev` `libssl-dev` `libcurl4-openssl-dev`.
+**Windows** is not supported.
 
-If installing from MacOS, you will need to install the [developer tools Xcode](https://apps.apple.com/us/app/xcode/id497799835?mt=12).
+From an R session, first install `tiledb` from R-Universe, the latest release in CRAN is not yet available.
 
 ```r
 install.packages(
@@ -43,11 +45,24 @@ install.packages(
 )
 ```
 
-Then install `cellxgene.census` from R-Universe.
+Then in an R session install `cellxgene.census` from R-Universe.
 
 ```r
 install.packages(
   "cellxgene.census",
   repos=c('https://chanzuckerberg.r-universe.dev', 'https://cloud.r-project.org') 
 )
-```
+```
+
+To be able to export Census data to `Seurat` or `SingleCellExperiment` you also need to install their respective packages.
+
+```r
+# Seurat
+install.packages("Seurat")
+
+# SingleCellExperiment
+if (!require("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+
+BiocManager::install("SingleCellExperiment")
+```