docs update

pkgdown/index.md

@@ -24,7 +24,7 @@ Snapshots of sections in the [quarto](https://quarto.org)-based cancer predispos
 
 ### News
 
-* *May 2024*: **2.x.x release**
+* *June 2024*: **2.x.x release**
   - New HTML report generation and layout with [quarto](https://quarto.org/)
   - Excel output supported
   - Updated virtual gene panels (Genomics England PanelApp, Cancer Gene Census)

vignettes/CHANGELOG.Rmd

@@ -5,7 +5,7 @@ output: rmarkdown::html_document
 
 ## v2.0.0
 
-* Date: **2024-05-xx**
+* Date: **2024-06-xx**
 * Data updates
   * ClinVar
   * GWAS catalog

vignettes/annotation_resources.Rmd

@@ -16,7 +16,7 @@ output: rmarkdown::html_document
 
 ### Variant databases of clinical utility
   * [ClinVar](http://www.ncbi.nlm.nih.gov/clinvar/) - database of clinically related variants (June 2024)
-  * [CIViC](https://civicdb.org) - clinical interpretations of variants in cancer (June 6th 2024)
+  * [CIViC](https://civicdb.org) - clinical interpretations of variants in cancer (June 21st 2024)
 
 ### Protein domains/functional features
   * [UniProt/SwissProt KnowledgeBase](http://www.uniprot.org) - resource on protein sequence and functional information (2024_03)

vignettes/installation.Rmd

@@ -4,10 +4,9 @@ output: rmarkdown::html_document
 ---
 
 CPSR is distributed alongside the [Personal Cancer Genome Reporter (PCGR)](https://github.com/sigven/pcgr), so please follow
-the [PCGR installation steps](https://sigven.github.io/pcgr/articles/installation.html) to install CPSR.
+the [PCGR installation steps](https://sigven.github.io/pcgr/articles/installation.html) to install CPSR, either through [Docker](https://docs.docker.com/), [Apptainer/Singularity](https://apptainer.org/docs/user/latest/index.html), or [Conda](https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html).
 
-We recommend [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html)
-as the simplest framework to install PCGR and CPSR, using either a MacOS or a Linux platform.
+We recommend [Conda](https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html) as the simplest framework to install PCGR and CPSR, using either a MacOS or a Linux platform.
 
 Assuming you have installed the `pcgr` and `pcgrr` conda envs as described in the above links
 at e.g. `/home/user/projects/cpsr_proj1/conda/env/`, you can load the `pcgr` environment and check

vignettes/running.Rmd

@@ -214,7 +214,7 @@ cpsr \
 	 --force_overwrite
 ```
 
-Note that the example command also refers to the PCGR data bundle directory (*refdata_dir*), which contains the data bundle that are necessary for both *PCGR* and *CPSR*.
+Note that the example command refers to the PCGR data bundle directory (*refdata_dir*), which contains the data bundle that are necessary for both *PCGR* and *CPSR*.
 
 This command will produce the following output files in the _output_ folder: