Updated installation tutorial

crisprVerse · Aug 31, 2022 · cafc6e2 · cafc6e2
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diff --git a/Installation/README.Rmd b/Installation/README.Rmd
@@ -25,31 +25,27 @@ necessary for some of the [crisprVerse tutorials](https://github.com/crisprVerse
 The crisprVerse is supported for macOS, Linux and Windows machines.
 It requires R version >=4.2.1. Some of the third-party functionalities are not
 available for Windows machines (BWA alignment, and some of the scoring 
-functions). To download and install R, see 
-the [R-project website](https://www.r-project.org/).
+functions). To download and install R, follow the instructions on the  [R-project website](https://www.r-project.org/).
 
 ## Bioconductor versions
 
-The Bioconductor project has 2 concurrent versions: `release` and `devel`.
-Currently (August 2022), the release version is`3.15`, and the
-devel version is `3.16`. Release versions are created twice a year.
+The Bioconductor project has 2 concurrent branches: `release` and `devel`.
+Currently (August 2022), the release branch is `3.15`, and the
+devel branch is `3.16`. Release versions are created twice a year. See the 
+[Bioconductor install page](https://www.bioconductor.org/install/) for
+more information regarding Bioconductor versions.
 
-The current version of the crisprVerse was developed on the devel version
-of Bioconductor (`3.16`) to make sure it accesses all of the latest 
-developments. Earlier versions of some of our packages are available 
-on the release version, but we do not recommend using the release version
-as most of the functionalities described in the tutorials require
-devel functionalities.
-
-See the [Bioconductor install page](https://www.bioconductor.org/install/) for
-more information re. Bioconductor. 
+The crisprVerse ecosystem is currently available on the Bioconductor
+devel branch (`3.16`). Earlier versions of some of our packages are available 
+on the release branch, but we do not recommend using the release branch
+as most of the functionalities described in the tutorials require updated
+functionalities only available on the devel branch. 
 
 
 ## Installing the core crisprVerse packages
 
-The [crisprVerse package](https://github.com/crisprVerse/crisprVerse) installs
-the core crisprVerse packages in a single command from Bioconductor. Simply
-type in the following commands in an R session:
+Type in the following commands in an R session to install the core
+crisprVerse packages from the Bioconductor devel branch:
 
 
 ```{r, eval=FALSE}
@@ -60,9 +56,6 @@ BiocManager::install(version="devel")
 BiocManager::install("crisprVerse")
 ```
 
-Note that we specify the devel branch of Bioconductor so that we
-can use the latest functionalities.
-
 
 This will install the following packages:
 
@@ -130,21 +123,24 @@ BiocManager::install(version="devel")
 BiocManager::install("crisprBwa")
 ```
 
+The [crisprViz](https://github.com/crisprVerse/crisprViz) package is
+currently under review at Bioconductor, but can be installed directly 
+from GitHub:
 
+```{r, eval=FALSE}
+if (!requireNamespace("devtools", quietly = TRUE))
+    install.packages("devtools")
 
-
-
-# Reproducibility
-
-```{r}
-sessionInfo()
+devtools::install.packages("crisprVerse/crisprViz")
 ```
 
 
+
 # Reproducibility
 
 ```{r}
 sessionInfo()
 ```
 
+
 # References
diff --git a/Installation/README.md b/Installation/README.md
@@ -14,8 +14,6 @@ Jean-Philippe Fortin, Luke Hoberecht
     -   <a href="#installing-optional-packages"
         id="toc-installing-optional-packages">Installing optional packages</a>
 -   <a href="#reproducibility" id="toc-reproducibility">Reproducibility</a>
--   <a href="#reproducibility-1"
-    id="toc-reproducibility-1">Reproducibility</a>
 -   <a href="#references" id="toc-references">References</a>
 
 # Installation
@@ -29,31 +27,27 @@ tutorials](https://github.com/crisprVerse/Tutorials).
 The crisprVerse is supported for macOS, Linux and Windows machines. It
 requires R version \>=4.2.1. Some of the third-party functionalities are
 not available for Windows machines (BWA alignment, and some of the
-scoring functions). To download and install R, see the [R-project
-website](https://www.r-project.org/).
+scoring functions). To download and install R, follow the instructions
+on the [R-project website](https://www.r-project.org/).
 
 ## Bioconductor versions
 
-The Bioconductor project has 2 concurrent versions: `release` and
-`devel`. Currently (August 2022), the release version is`3.15`, and the
-devel version is `3.16`. Release versions are created twice a year.
+The Bioconductor project has 2 concurrent branches: `release` and
+`devel`. Currently (August 2022), the release branch is `3.15`, and the
+devel branch is `3.16`. Release versions are created twice a year. See
+the [Bioconductor install page](https://www.bioconductor.org/install/)
+for more information regarding Bioconductor versions.
 
-The current version of the crisprVerse was developed on the devel
-version of Bioconductor (`3.16`) to make sure it accesses all of the
-latest developments. Earlier versions of some of our packages are
-available on the release version, but we do not recommend using the
-release version as most of the functionalities described in the
-tutorials require devel functionalities.
-
-See the [Bioconductor install
-page](https://www.bioconductor.org/install/) for more information re.
-Bioconductor.
+The crisprVerse ecosystem is currently available on the Bioconductor
+devel branch (`3.16`). Earlier versions of some of our packages are
+available on the release branch, but we do not recommend using the
+release branch as most of the functionalities described in the tutorials
+require updated functionalities only available on the devel branch.
 
 ## Installing the core crisprVerse packages
 
-The [crisprVerse package](https://github.com/crisprVerse/crisprVerse)
-installs the core crisprVerse packages in a single command from
-Bioconductor. Simply type in the following commands in an R session:
+Type in the following commands in an R session to install the core
+crisprVerse packages from the Bioconductor devel branch:
 
 ``` r
 if (!requireNamespace("BiocManager", quietly = TRUE))
@@ -63,9 +57,6 @@ BiocManager::install(version="devel")
 BiocManager::install("crisprVerse")
 ```
 
-Note that we specify the devel branch of Bioconductor so that we can use
-the latest functionalities.
-
 This will install the following packages:
 
 -   [crisprBase](https://github.com/crisprVerse/crisprBase) to specify
@@ -133,31 +124,16 @@ BiocManager::install(version="devel")
 BiocManager::install("crisprBwa")
 ```
 
-# Reproducibility
+The [crisprViz](https://github.com/crisprVerse/crisprViz) package is
+currently under review at Bioconductor, but can be installed directly
+from GitHub:
 
 ``` r
-sessionInfo()
-```
+if (!requireNamespace("devtools", quietly = TRUE))
+    install.packages("devtools")
 
-    ## R version 4.2.1 (2022-06-23)
-    ## Platform: x86_64-apple-darwin17.0 (64-bit)
-    ## Running under: macOS Catalina 10.15.7
-    ## 
-    ## Matrix products: default
-    ## BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
-    ## LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
-    ## 
-    ## locale:
-    ## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
-    ## 
-    ## attached base packages:
-    ## [1] stats     graphics  grDevices utils     datasets  methods   base     
-    ## 
-    ## loaded via a namespace (and not attached):
-    ##  [1] compiler_4.2.1   magrittr_2.0.3   fastmap_1.1.0    cli_3.3.0       
-    ##  [5] tools_4.2.1      htmltools_0.5.3  rstudioapi_0.14  yaml_2.3.5      
-    ##  [9] stringi_1.7.8    rmarkdown_2.15.2 knitr_1.40       stringr_1.4.1   
-    ## [13] xfun_0.32        digest_0.6.29    rlang_1.0.4      evaluate_0.16
+devtools::install.packages("crisprVerse/crisprViz")
+```
 
 # Reproducibility
 

diff --git a/Installation/README.pdf b/Installation/README.pdf