Merge pull request #621 from satijalab/fix/sct2vig

Update sct2 vignette installation instructions

Author: mojaveazure

vignettes/sctransform_v2_vignette.Rmd

@@ -35,12 +35,12 @@ knitr::opts_chunk$set(
 
 We recently introduced [sctransform](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1874-1) to perform normalization and variance stabilization of scRNA-seq datasets. We now release an updated version ('v2'), based on [our broad analysis](https://www.biorxiv.org/content/10.1101/2021.07.07.451498v1) of 59 scRNA-seq datasets spanning a range of technologies, systems, and sequencing depths. This update improves speed and memory consumption, the stability of parameter estimates, the identification of variable features, and the the ability to perform downstream differential expression analyses.
 
-Users can install sctransform v2 from Github (CRAN update coming soon), and invoke the use of the updated method via the `vst.flavor` argument.
+Users can install sctransform v2 from CRAN (sctransform v0.3.3) and invoke the use of the updated method via the `vst.flavor` argument.
 
 ```{r tldr, eval=FALSE}
-# install Seurat from Github (automatically updates sctransform)
-devtools::install_github("satijalab/seurat", ref="develop") 
-# invoke sctransform
+# install sctransform >= 0.3.3
+install.packages("sctransform") 
+# invoke sctransform - requires Seurat>=4.1
 object <- SCTransform(object, vst.flavor = "v2")
 ```
 
@@ -56,14 +56,14 @@ In this vignette, we use [sctransform v2](https://github.com/satijalab/sctransfo
 
 ## Install sctransform
 
-We will install sctransform v2 from Github. We will also install the [glmGamPoi](https://bioconductor.org/packages/release/bioc/html/glmGamPoi.html) package which substantially improves the speed of the learning procedure. 
+We will install sctransform v2 from CRAN (v0.3.3). We will also install the [glmGamPoi](https://bioconductor.org/packages/release/bioc/html/glmGamPoi.html) package which substantially improves the speed of the learning procedure. 
 
 ```{r results='hide', message=FALSE, warning=FALSE}
 # install glmGamPoi
 if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
 BiocManager::install("glmGamPoi")
 # install sctransform from Github
-devtools::install_github("satijalab/sctransform", ref="develop") 
+install.packages("sctransform") 
 ```
 
 ## Setup the Seurat objects