Changes between Version 55 and Version 56 of SOP/scRNA-seq


Ignore:
Timestamp:
04/18/24 14:47:01 (10 months ago)
Author:
xinlei.gao
Comment:

Add a section at the beginning to specify the version of Seurat package.

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  • SOP/scRNA-seq

    v55 v56  
    11
    22== Single cell RNA-Seq to quantify gene levels and assay for differential expression ==
     3
     4=== Load appropriate version of the Seurat package ===
     5
     6As of April 18, 2024, the default version of Seurat available on fry/RStudio is v5.0.1.
     7
     8To use Seurat version 5, enter the following command in R:
     9{{{
     10library(Seurat)
     11}}}
     12In some instances, certain software may only be compatible with older versions of Seurat, or you might need to run analyses on Seurat objects created with earlier versions. In these cases, you can load an earlier version of Seurat by specifying the library location.
     13
     14For example, to load Seurat version 4, use this command:
     15{{{
     16require(Seurat, lib.loc="/nfs/apps/lib/R/4.2-focal/site-library.2023q1/")
     17}}}
     18This command directs R to use a specific library path where Seurat version 4 is installed, ensuring compatibility with older datasets or software requirements.
    319
    420=== Create a matrix of gene counts by cells ===