Clean up documentation

igordot · Oct 14, 2022 · a1d20aa · a1d20aa
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diff --git a/LICENSE b/LICENSE
@@ -1,2 +1,2 @@
-YEAR: 2018-2021
+YEAR: 2018-2022
 COPYRIGHT HOLDER: Igor Dolgalev
diff --git a/LICENSE.md b/LICENSE.md
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2018-2021
+Copyright (c) 2018-2022
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/README.md b/README.md
@@ -2,17 +2,17 @@
 
 [![CRAN](https://www.r-pkg.org/badges/version/msigdbr)](https://cran.r-project.org/package=msigdbr)
 [![CRAN downloads](https://cranlogs.r-pkg.org/badges/last-month/msigdbr)](https://cran.r-project.org/package=msigdbr)
-[![R build status](https://github.com/igordot/msigdbr/workflows/R-CMD-check/badge.svg)](https://github.com/igordot/msigdbr/actions)
+[![R-CMD-check](https://github.com/igordot/msigdbr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/igordot/msigdbr/actions/workflows/R-CMD-check.yaml)
 [![codecov](https://codecov.io/gh/igordot/msigdbr/branch/master/graph/badge.svg)](https://app.codecov.io/gh/igordot/msigdbr)
 
 ## Overview
 
-The `msigdbr` R package provides Molecular Signatures Database (MSigDB) gene sets typically used with the Gene Set Enrichment Analysis (GSEA) software:
+The msigdbr R package provides Molecular Signatures Database (MSigDB) gene sets typically used with the Gene Set Enrichment Analysis (GSEA) software:
 
-* in an R-friendly tidy/long format with one gene per row
+* in an R-friendly "[tidy](https://r4ds.had.co.nz/tidy-data.html)" format with one gene pair per row
 * for multiple frequently studied model organisms, such as mouse, rat, pig, zebrafish, fly, and yeast, in addition to the original human genes
 * as gene symbols as well as NCBI Entrez and Ensembl IDs
-* that can be installed and loaded as a package without requiring additional external files
+* without accessing external resources and requiring an active internet connection
 
 ## Installation
 
@@ -30,4 +30,4 @@ The package data can be accessed using the `msigdbr()` function, which returns a
 genesets = msigdbr(species = "Mus musculus", category = "C2", subcategory = "CGP")
 ```
 
-Check the [documentation website](https://igordot.github.io/msigdbr/) for more information.
+Check the [documentation website](https://igordot.github.io/msigdbr/articles/msigdbr-intro.html) for more information.
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -1,15 +1,26 @@
-url: https://igordot.github.io/msigdbr
+url: https://igordot.github.io/msigdbr/
 
 template:
-  params:
-    bootswatch: readable
-    ganalytics: UA-130263433-2
+  bootstrap: 5
+  bootswatch: zephyr
+  includes:
+    before_body: |
+       <!-- Global site tag (gtag.js) - Google Analytics -->
+       <script async src="https://www.googletagmanager.com/gtag/js?id=G-WW0CJR3Z9Z"></script>
+       <script>
+         window.dataLayer = window.dataLayer || [];
+         function gtag(){dataLayer.push(arguments);}
+         gtag('js', new Date());
+
+         gtag('config', 'G-WW0CJR3Z9Z');
+       </script>
   opengraph:
     twitter:
       creator: "@bioigor"
       card: summary_large_image
 
 navbar:
+  bg: light
   structure:
     left: []
     right: [home, intro, reference, articles, news, github]
@@ -22,4 +33,3 @@ navbar:
 
 home:
   title: MSigDB gene sets R package
-  strip_header: true