update descrition and add vignette

.Rbuildignore

@@ -1,3 +1,5 @@
+^renv$
+^renv\.lock$
 ^LICENSE\.md$
 .github
 Dockerfile

.gitignore

@@ -2,3 +2,6 @@ inst/doc
 *~
 .Rproj.user
 *Rproj
+renv/
+renv.lock
+.Rprofile

DESCRIPTION

@@ -1,27 +1,49 @@
-Package: BuildABiocWorkshop
-Title: Bioconductor or R Workshop Template and Github Actions
+Package: iSEEDemoEuroBioC2024
+Title: Package demo for EuroBioC2024
 Version: 2.0.1
 Authors@R: 
-    person(given = "Sean",
-           family = "Davis",
-           role = c("aut", "cre"),
-           email = "seandavi@gmail.com",
-           comment = c(ORCID = "0000-0002-8991-6458"))
-Description: This package serves as a template for using github actions to 
-    prepare a Bioconductor Workshop package for use. In particular,
-    a pkgdown website and docker image are generated based on workflow 
-    settings. 
+    c(person(given = "Federico",
+             family = "Marini",
+             role = c("aut", "cre"),
+             email = "marinif@uni-mainz.de",
+             comment = c(ORCID = "0000-0003-3252-7758")),
+      person(given = "Charlotte",
+             family = "Soneson",
+             role = "aut",
+             email = "charlottesoneson@gmail.com",
+             comment = c(ORCID = "0000-0003-3833-2169")),
+      person(given = "Kevin",
+             family = "Rue-Albrecht",
+             role = "aut",
+             email = "kevinrue67@gmail.com",
+             comment = c(ORCID = "0000-0003-3899-3872"))
+     )
+Description: This package provides the environment and materials for the
+    package demo at the European Bioconductor Meeting 2024.
+    The environment includes the iSEE package and all its extensions
+    developed under the iSEE organisation.
+    The materials provide a brief overview of the core package functionality,
+    and a walkthrough of the development of an example extension package.
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.1.0
 Depends: 
     Biobase
+Imports:
+    iSEE,
+    iSEEde,
+    iSEEhex,
+    iSEEhub,
+    iSEEindex,
+    iSEEpathways,
+    iSEEu
 Suggests: 
     knitr,
     rmarkdown,
-    pkgdown
+    pkgdown,
+    BiocStyle
 URL: https://seandavi.github.io/BuildABiocWorkshop/
 BugReports: https://github.com/seandavi/BuildABiocWorkshop/issues/new/choose
 VignetteBuilder: knitr

vignettes/workshop_isee_extension.Rmd

@@ -0,0 +1,112 @@
+---
+title: "Writing an iSEE extension"
+author: Kevin Rue-Albrecht^[kevinrue67@gmail.com],Federico Marini^[marinif@uni-mainz.de], Charlotte Soneson^[charlottesoneson@gmail.com]
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Writing an iSEE extension}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+# Writing an iSEE extension
+
+Authors:
+    Kevin Rue-Albrecht^[University of Oxford],
+    Federico Marini^[Johannes Gutenberg-Universität Mainz],
+    Charlotte Soneson^[Friedrich Miescher Institute for Biomedical Research].
+    <br/>
+Last modified: 09 July, 2024.
+
+## Overview
+
+### Description
+
+This package demo will present a brief introduction to the functionality of the
+iSEE package and its existing extension packages, before demonstrating the
+writing of new functionality suitable for release in additional extension
+packages.
+
+### Pre-requisites
+
+* Familiarity with the SummarizedExperiment class.
+* Familiarity with the shiny package
+
+List any workshop prerequisites, for example:
+
+* Basic knowledge of R syntax
+* Familiarity with the GenomicRanges class
+* Familiarity with xyz vignette (provide link)
+
+List relevant background reading for the workshop, including any
+theoretical background you expect students to have.
+
+* List any textbooks, papers, or other reading that students should be
+  familiar with. Include direct links where possible.
+
+### Participation
+
+Describe how students will be expected to participate in the workshop.
+
+### _R_ / _Bioconductor_ packages used
+
+List any _R_ / _Bioconductor_ packages that will be explicitly covered.
+
+### Time outline
+
+An example for a 45-minute workshop:
+
+| Activity                     | Time |
+|------------------------------|------|
+| Packages                     | 15m  |
+| Package Development          | 15m  |
+| Contributing to Bioconductor | 5m   |
+| Best Practices               | 10m  |
+
+### Workshop goals and objectives
+
+List "big picture" student-centered workshop goals and learning
+objectives. Learning goals and objectives are related, but not the
+same thing. These goals and objectives will help some people to decide
+whether to attend the conference for training purposes, so please make
+these as precise and accurate as possible.
+
+*Learning goals* are high-level descriptions of what
+participants will learn and be able to do after the workshop is
+over. *Learning objectives*, on the other hand, describe in very
+specific and measurable terms specific skills or knowledge
+attained. The [Bloom's Taxonomy](#bloom) may be a useful framework
+for defining and describing your goals and objectives, although there
+are others.
+
+### Learning goals
+
+Some examples:
+
+* describe how to...
+* identify methods for...
+* understand the difference between...
+
+### Learning objectives
+
+* analyze xyz data to produce...
+* create xyz plots
+* evaluate xyz data for artifacts
+
+## Workshop
+
+Divide the workshop into sections (`## A Section`). Include
+fully-evaluated _R_ code chunks. Develop exercises and solutions, and
+anticipate that your audience will walk through the code with you, or
+work on the code idependently -- do not be too ambitious in the
+material that you present.
+
+
+