Release v1.0.0

Merge into Main

.github/workflows/pages.yml

@@ -63,7 +63,7 @@ jobs:
         run: bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}"
         env:
           JEKYLL_ENV: production
-          PAGES_REPO_NWO: leaseep/OmicShiny
+          PAGES_REPO_NWO: icb-dcm/cOmicsArt
 
       - name: Upload artifact
         # Automatically uploads an artifact from the './_site' directory by default

.github/workflows/start_check.yaml

@@ -34,7 +34,8 @@ jobs:
       shell: Rscript {0}
       run: |
         install.packages("renv")
-        renv::restore()
+        print(getwd())
+        renv::restore(lockfile="program/renv.lock")
         
     # - name: Get R and OS version
     #   id: get-version

README.md

@@ -1,20 +1,33 @@
-# Data Input Notes:
+# Welcome to cOmicsArt
+
+![comic of a wombat on the path to find this
+Readme](docs/assets/images/cOmicsART_README.png)
+*Image generated using DALL-E by OpenAI. Adjusted by Lea Seep*
+
+Please refer to the following listed links for further information on
+the respective topics:
+
 ## Status Quo
+
 General Test:
-![example workflow](https://github.com/LeaSeep/OmicShiny/actions/workflows/run-tests.yaml/badge.svg)
-
-Develop-Version Test-Status:
-![develop status](https://github.com/LeaSeep/OmicShiny/actions/workflows/run-tests.yaml/badge.svg?branch=develop)
-
-Main-Version Test-Status:
-![main status](https://github.com/LeaSeep/OmicShiny/actions/workflows/run-tests.yaml/badge.svg?branch=main)
-
-3 tables are needed:
-1. data-table (e.g. counts or intensitites)
-  - row names must be entities (e.g. genes or metabolites)
-  - column names must be sample names
-2. sample annotation (e.g. Treatment, tissue type) 
-  - rownames must match the colnames from (1.), hence each sample get a row
-  - MUST have a column called global_ID (same as rownames) with unique entries
-3. entitie annotation (e.g. type of gene or assoc pathway of metab)
-  - rownames must match the rownames from (1.)
+[![Repository Status](https://github.com/ICB-DCM/cOmicsArt/actions/workflows/start_check.yaml/badge.svg)](https://github.com/ICB-DCM/cOmicsArt/actions/workflows/start_check.yaml)
+
+[![Deploy Jekyll site to Pages](https://github.com/ICB-DCM/cOmicsArt/actions/workflows/pages.yml/badge.svg)](https://github.com/ICB-DCM/cOmicsArt/actions/workflows/pages.yml)
+
+-   cOmicsArt is freely available at
+    <https://shiny.iaas.uni-bonn.de/cOmicsArt/>
+
+-   User documentation is available at
+    <https://icb-dcm.github.io/cOmicsArt/>
+
+-   A docker image can be retrieved from
+    <https://hub.docker.com/r/pauljonasjost/comicsart/tags>
+
+-   A screen recording of cOmicsArt is available at
+    <https://www.youtube.com/watch?v=pTGjtIYQOak>
+
+-   A snapshot upon publication can be found on Zenodo: very last thing;
+    Note, that you can find within the branches the Zenodo based
+    branches.
+
+Have fun!

docs/Gemfile.lock

@@ -68,7 +68,14 @@ GEM
       tzinfo (~> 2.0)
     addressable (2.8.7)
       public_suffix (>= 2.0.2, < 7.0)
+    bibtex-ruby (4.4.7)
+      latex-decode (~> 0.0)
     builder (3.3.0)
+    citeproc (1.0.10)
+      namae (~> 1.0)
+    citeproc-ruby (1.1.14)
+      citeproc (~> 1.0, >= 1.0.9)
+      csl (~> 1.6)
     coffee-script (2.4.1)
       coffee-script-source
       execjs
@@ -77,6 +84,11 @@ GEM
     commonmarker (0.23.10)
     concurrent-ruby (1.3.3)
     crass (1.0.6)
+    csl (1.6.0)
+      namae (~> 1.0)
+      rexml
+    csl-styles (1.0.1.11)
+      csl (~> 1.0)
     date (3.3.4)
     dnsruby (1.72.1)
       simpleidn (~> 0.2.1)
@@ -209,6 +221,11 @@ GEM
       rubyzip (>= 1.3.0, < 3.0)
     jekyll-sass-converter (1.5.2)
       sass (~> 3.4)
+    jekyll-scholar (5.16.0)
+      bibtex-ruby (~> 4.0, >= 4.0.13)
+      citeproc-ruby (~> 1.0)
+      csl-styles (~> 1.0)
+      jekyll (~> 3.0)
     jekyll-seo-tag (2.8.0)
       jekyll (>= 3.8, < 5.0)
     jekyll-sitemap (1.4.0)
@@ -271,6 +288,7 @@ GEM
       rexml
     kramdown-parser-gfm (1.1.0)
       kramdown (~> 2.0)
+    latex-decode (0.4.0)
     liquid (4.0.4)
     listen (3.9.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
@@ -292,6 +310,8 @@ GEM
       jekyll-feed (~> 0.9)
       jekyll-seo-tag (~> 2.1)
     minitest (5.24.0)
+    namae (1.2.0)
+      racc (~> 1.7)
     net-http (0.4.1)
       uri
     net-imap (0.3.7)
@@ -387,6 +407,7 @@ DEPENDENCIES
   github-pages
   jekyll
   jekyll-remote-theme
+  jekyll-scholar
   jekyll-seo-tag
   just-the-docs
   nokogiri

docs/_config.yml

@@ -3,8 +3,8 @@
 title: cOmicsART Documentation
 logo: "/assets/images/Logo_cOmicsArt.svg"  # Update to the new image file path
 description: Here you find all the information you need to use cOmicsART
-baseurl: "/OmicShiny"
-url: "https://leaseep.github.io/"
+baseurl: "/cOmicsART"
+url: "https://icb-dcm.github.io/"
 #theme: just-the-docs
 remote_theme: just-the-docs/just-the-docs
 

docs/code-and-data.md

@@ -5,6 +5,16 @@ has_children: true
 nav_order: 3
 ---
 
+# Code and Data download
 
-![A comic about a cat finding cOmicsART](/OmicShiny/assets/images/cOmicsPenguin.png)
-*Image generated using DALL-E by OpenAI. Adjusted by Lea Seep*
+![A comic about a cat finding cOmicsART](/cOmicsArt/assets/images/cOmicsPenguin.png)
+*Image generated using DALL-E by OpenAI. Adjusted by Lea Seep*
+
+cOmicsArt allows you to reproduce your analysis not only **within** the application 
+through the report, but also independently of the application using provided R code. 
+This not only guarantees the reproducibility of your analysis, but also allows you to 
+easily adjust your analysis to your needs.
+
+This page provides information regarding the Code and Data download for 
+cOmicsART. We explain the [general code structure](code-and-data/r-code.md) and provide an [example how to adjust the code](code-and-data/examples.md). Note that the adjusted code is only exemplary 
+and not exhaustive. We encourage you to explore the code and adjust it to your needs.