update installation instructions

BorchLab · Nov 4, 2024 · abe1b94 · abe1b94
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diff --git a/README.md b/README.md
@@ -29,7 +29,7 @@ devtools::install_github("ncborcherding/scRepertoire")
 ```
 
 ### Installing from Bioconductor
-The current version of scRepertoire is also available on [Bioconductor](https://bioconductor.org/packages/3.19/bioc/html/scRepertoire.html).
+The current version of scRepertoire is also available on [Bioconductor](https://www.bioconductor.org/packages/release/bioc/html/scRepertoire.html).
 
 ```R
 if (!require("BiocManager", quietly = TRUE))
@@ -47,7 +47,7 @@ devtools::install_github("ncborcherding/scRepertoire@v1")
 
 ## Getting Data
 
-Unfortunately, Github limits the size of individual files. In order to access the seurat object paired with scRepertoire please download the .rda from [here](https://drive.google.com/file/d/1_YuRraDyg8UgF3oasjF0-jgPnwox-B24/view?usp=share_link).
+Unfortunately, Github limits the size of individual files. In order to access the Seurat object paired with scRepertoire please download the .rda from [here](https://drive.google.com/file/d/1_YuRraDyg8UgF3oasjF0-jgPnwox-B24/view?usp=share_link).
 
 ## Bug Reports/New Features
 
@@ -62,4 +62,8 @@ be extremely helpful.
 #### [Pull Requests](https://github.com/ncborcherding/scRepertoire/pulls) are welcome for bug fixes, new features, or enhancements.
 
 ## Please Cite
-Feel free to use, edit, modify scRepertoire, but if you do, please cite the [manuscript](https://f1000research.com/articles/9-47/v1). If you are building your own tool based on scRepertoire, reach out, I am happy to help and make things compatible.
+We are working on submitting the scRepertoire v2 as a peer review article. For now, please cite scRepertoire using the doi from [Bioconductor](https://www.bioconductor.org/packages/release/bioc/html/scRepertoire.html).
+
+*Borcherding, N, Yang, Q, & Safina, K. (2024). scRepertoire v2: A toolkit for single-cell immune receptor profiling. DOI: 10.18129/B9.bioc.scRepertoire*
+
+If you are building your own tool based on scRepertoire, reach out, I am happy to help and make things compatible.
diff --git a/index.md b/index.md
@@ -39,7 +39,9 @@ Unfortunately, Github limits the size of individual files. In order to access th
 
 ## Please Cite
 
-We are working on submitting the scRepertoire v2 as a peer review article.
+We are working on submitting the scRepertoire v2 as a peer review article. For now, please cite scRepertoire using the doi from [Bioconductor](https://www.bioconductor.org/packages/release/bioc/html/scRepertoire.html).
+
+*Borcherding, N, Yang, Q, & Safina, K. (2024). scRepertoire v2: A toolkit for single-cell immune receptor profiling. DOI: 10.18129/B9.bioc.scRepertoire*
 
 ## Bug Reports/New Features
 

diff --git a/inst/pkgdown.yml b/inst/pkgdown.yml
@@ -20,7 +20,7 @@ articles:
   articles/SC_Visualizations: SC_Visualizations.html
   articles/Trex: Trex.html
   vignette: vignette.html
-last_built: 2024-11-04T17:59Z
+last_built: 2024-11-04T18:54Z
 urls:
   reference: https://www.borch.dev/uploads/scRepertoire/reference
   article: https://www.borch.dev/uploads/scRepertoire/articles
diff --git a/vignettes/articles/Installation.Rmd b/vignettes/articles/Installation.Rmd
@@ -55,11 +55,9 @@ remotes::install_github(repo = "ncborcherding/scRepertoire", ref = "dev")
 
 ## Bioconductor
 
-The current version of scRepertoire is also available in the development version of Bioconductor. Important to note, the version is listed as 1.99.1 on [Bioconductor](https://bioconductor.org/packages/3.19/bioc/html/scRepertoire.html) per their version guidelines.
+The current version of scRepertoire is also available in the development version of Bioconductor. 
 
 ```
-BiocManager::install(version='devel')
-
 BiocManager::install("scRepertoire")
 ```