Skip to content

Commit

Permalink
Release v1.0.0
Browse files Browse the repository at this point in the history
Merge into Main
  • Loading branch information
PaulJonasJost authored Sep 10, 2024
2 parents 45d6839 + 49b6ff1 commit 9943743
Show file tree
Hide file tree
Showing 62 changed files with 2,058 additions and 4,619 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/pages.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
3 changes: 2 additions & 1 deletion .github/workflows/start_check.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
49 changes: 31 additions & 18 deletions README.md
Original file line number Diff line number Diff line change
@@ -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!
21 changes: 21 additions & 0 deletions docs/Gemfile.lock
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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)
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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)
Expand All @@ -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)
Expand Down Expand Up @@ -387,6 +407,7 @@ DEPENDENCIES
github-pages
jekyll
jekyll-remote-theme
jekyll-scholar
jekyll-seo-tag
just-the-docs
nokogiri
Expand Down
4 changes: 2 additions & 2 deletions docs/_config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down
Binary file added docs/assets/images/DataInputShiny.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/assets/images/Figure4.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/assets/images/FigureD1.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/assets/images/FigureD2.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/assets/images/FigureD3.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/assets/images/FigureD5.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/assets/images/FigureD6.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/assets/images/FigureD7.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/assets/images/FigureD8.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/assets/images/FigureE1.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/assets/images/FigureE2.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/assets/images/FigureE3.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/assets/images/Slideshow1.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/assets/images/Slideshow2.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/assets/images/Slideshow3.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/assets/images/Slideshow4.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/assets/images/cOmicsART_README.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/assets/images/volcano_plot_comparison.pdf
Binary file not shown.
Binary file added docs/assets/images/volcano_plot_original.pdf
Binary file not shown.
Binary file added docs/assets/images/volcano_plot_theme.pdf
Binary file not shown.
Binary file added docs/assets/images/volcano_plot_thresholds.pdf
Binary file not shown.
14 changes: 12 additions & 2 deletions docs/code-and-data.md
Original file line number Diff line number Diff line change
Expand Up @@ -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.
6 changes: 0 additions & 6 deletions docs/code-and-data/data.md

This file was deleted.

Loading

0 comments on commit 9943743

Please sign in to comment.