diff --git a/.Rbuildignore b/.Rbuildignore
index 634bd55..d42b9e1 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -16,3 +16,4 @@ README.rst
^notebooks/
man-roxygen
^\.github$
+^pkgdown$
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
new file mode 100644
index 0000000..174e23d
--- /dev/null
+++ b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,48 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+ push:
+ branches: [devel]
+ pull_request:
+ branches: [devel]
+ release:
+ types: [published]
+ workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+ pkgdown:
+ runs-on: ubuntu-latest
+ # Only restrict concurrency for non-PR jobs
+ concurrency:
+ group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ permissions:
+ contents: write
+ steps:
+ - uses: actions/checkout@v3
+
+ - uses: r-lib/actions/setup-pandoc@v2
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: any::pkgdown, local::.
+ needs: website
+
+ - name: Build site
+ run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+ shell: Rscript {0}
+
+ - name: Deploy to GitHub pages 🚀
+ if: github.event_name != 'pull_request'
+ uses: JamesIves/github-pages-deploy-action@v4.4.1
+ with:
+ clean: false
+ branch: gh-pages
+ folder: docs
diff --git a/.gitignore b/.gitignore
index 6111e2b..d7306ae 100644
--- a/.gitignore
+++ b/.gitignore
@@ -16,3 +16,4 @@ vignettes/.build.timestamp
doc
vignettes/Bioconductor.sty
vignettes/unsrturl.bst
+docs
diff --git a/DESCRIPTION b/DESCRIPTION
index d179d03..9ee01c6 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -147,5 +147,5 @@ Suggests: agricolae,
rappdirs
VignetteBuilder: knitr
biocViews: WorkflowStep, Metabolomics
-URL: https://github.com/computational-metabolomics/structToolbox
+URL: https://github.com/computational-metabolomics/structToolbox, https://computational-metabolomics.github.io/structToolbox/
Roxygen: list(markdown = TRUE)
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..6921b52
--- /dev/null
+++ b/README.md
@@ -0,0 +1,44 @@
+# structToolbox
+
+An extensive set of data (pre-)processing and analysis methods and
+tools for metabolomics and other omics, with a strong emphasis on statistics and
+machine learning.
+
+This toolbox allows the user to build extensive and
+standardised workflows for data analysis. The methods and tools have been
+implemented using class-based templates provided by the `struct` (Statistics
+in R Using Class-based Templates) package.
+The toolbox includes pre-processing
+methods (e.g. signal drift and batch correction, normalisation, missing value
+imputation and scaling), univariate (e.g. ttest, various forms of ANOVA,
+Kruskal–Wallis test and more) and multivariate statistical methods (e.g. PCA and
+PLS, including cross-validation and permutation testing) as well as machine
+learning methods (e.g. Support Vector Machines). The
+STATistics Ontology (STATO) has been integrated and implemented to provide
+standardised definitions for the different methods, inputs and outputs.
+
+## Installation
+
+To install this package:
+
+```
+if (!require("BiocManager", quietly = TRUE))
+ install.packages("BiocManager")
+
+BiocManager::install("structToolbox")
+```
+
+To install the development version:
+
+```
+if (!require("remotes", quietly = TRUE))
+ install.packages("remotes")
+
+remotes::install_github("computational-metabolomics/structToolbox")
+```
+
+
+[![BioC version](https://img.shields.io/badge/dynamic/yaml?url=https%3A%2F%2Fbioconductor.org%2Fconfig.yaml&query=%24.release_version&label=Bioconductor)](http://www.bioconductor.org)
+[![BioC status](http://www.bioconductor.org/shields/build/release/bioc/structToolbox.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/structToolbox)
+
+
\ No newline at end of file
diff --git a/README.rst b/README.rst
deleted file mode 100644
index 3de4941..0000000
--- a/README.rst
+++ /dev/null
@@ -1,50 +0,0 @@
-==============================================
-structToolbox
-==============================================
-
-|Git| |Bioconda| |Build Status| |License| |Coverage| |mybinder|
-
-
-------------
-Install
-------------
-
-
-Github
-------------
-
-.. code-block:: r
-
- library(devtools)
- library(testthat)
- install_github('computational-metabolomics/structToolbox')
-
-Conda
-------------
-
-.. code-block:: command
-
- conda create -n structtoolbox bioconductor-structtoolbox -c conda-forge -c bioconda
- conda activate structtoolbox
-
-------------
-References
-------------
-
-.. |Build Status| image:: https://github.com/computational-metabolomics/structToolbox/workflows/structToolbox/badge.svg
- :target: https://github.com/computational-metabolomics/structToolbox/actions
-
-.. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=3600
- :target: https://github.com/computational-metabolomics/structToolbox
-
-.. |Bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat&maxAge=3600
- :target: https://bioconda.github.io/recipes/bioconductor-structtoolbox/README.html
-
-.. |License| image:: https://img.shields.io/badge/licence-GNU_v3-teal.svg?style=flat&maxAge=3600
- :target: https://www.gnu.org/licenses/gpl-3.0.html
-
-.. |Coverage| image:: https://codecov.io/gh/computational-metabolomics/structToolbox/branch/master/graph/badge.svg
- :target: https://codecov.io/gh/computational-metabolomics/structToolbox
-
-.. |mybinder| image:: https://mybinder.org/badge_logo.svg
- :target: https://mybinder.org/v2/gh/computational-metabolomics/structToolbox/master?filepath=notebooks
diff --git a/_pkgdown.yml b/_pkgdown.yml
new file mode 100644
index 0000000..eccc417
--- /dev/null
+++ b/_pkgdown.yml
@@ -0,0 +1,6 @@
+url: https://computational-metabolomics.github.io/structToolbox/
+template:
+ bootstrap: 5
+ bootswatch: flatly
+
+