Changes between Version 56 and Version 57 of SOP/scRNA-seq

Timestamp:

04/23/24 14:24:39 (20 months ago)

Author:

xinlei.gao

Comment:

--

SOP/scRNA-seq

@@ -17 +17 @@
 }}}
 This command directs R to use a specific library path where Seurat version 4 is installed, ensuring compatibility with older datasets or software requirements.
+
+However, sometimes Seurat may depend on other R packages to run certain functions, in that case, only loading the older version of Seurat may not work. Instead, we could explicitly load all R packages from the last R library set to keep the packages compatible.
+{{{
+set_lib_paths <- function(lib_vec) {
+  lib_vec <- normalizePath(lib_vec, mustWork = TRUE)
+  shim_fun <- .libPaths
+  shim_env <- new.env(parent = environment(shim_fun))
+  shim_env$.Library <- character()
+  shim_env$.Library.site <- character()
+  environment(shim_fun) <- shim_env
+  shim_fun(lib_vec)
+}
+
+set_lib_paths(c("/nfs/apps/lib/R/4.2-focal/site-library.2023q1", "/opt/R/4.2.1/lib/R/library"))
+
+library(Seurat)
+# load other required packages, e.g. scPred, for cell type annotation.
+library(scPred)
+}}}
+
+By running the codes above, all the required R packages will be loaded from the previous R library set (2023q1).
 
 === Create a matrix of gene counts by cells ===