This repo contains the course material for NBIS course Workshop on RNA-Seq. The rendered view of this repo is available here.
To add or update contents of this repo (for collaborators), first clone the repo.
git clone https://github.com/nbisweden/course_rnaseq.git
Make changes/updates as needed. Add the changed files. Commit it. Then push the repo back.
git add *
git commit -m "I did this and that"
git status
git push origin
If you are not added as a collaborator, first fork this repo to your account, then clone it locally, make changes, commit, push to your repo, then submit a pull request to this repo.
These are descriptions of the files and a guide to updating this repo for course maintainers.
_site.yml
All website configuration options are here. Nothing to be changed here.
README.md
You are reading this file now. Nothing to do here.
index.Rmd
This file generates the home page. Make sure that the date and location is correct. Verify links.
schedule.Rmd
This file generates the schedule page. The start time of the course is set to 09:00:00. Change if needed. It is assumed that the course starts at the same time everyday.
schedule.csv
This table holds the schedule information. Open/edit in a spreadsheet or text editor. Columns are delimited by ;. Do not change the number of columns, position of columns or column names.
date: Full date for each day in format dd/mm/yyyy. Missing/empty cells are filled down automatically.
room: Room number for the course. Missing/empty cells are filled down automatically.
dur: Duration for the topic in minutes.
topic: Topic name (Keep it short).
person: Name of the person covering the topic.
link_presentation: (Optional) Link to the presentation. Local links can be just presentation_topic.html. Use this labelling convention.
link_lab: (Optional) Link to the lab material. Local links can be just lab_topic.html. This is the labelling convention used.
link_room: (Optional) Link to the room location. Can be a google map link, mazemap link etc.
lab.Rmd
This page brings together all the exercises. Verify links.
precourse.Rmd
This page holds the steps needed to be completed before the course. Change project ID for each course.
info.Rmd
This page contains practical information related to the course. Set location and update info if needed.
[presentation_topic.Rmd]
RMarkdown presentation files for various topics. Replace 'topic' with a short name of the topic.
[lab_topic.Rmd]
RMarkdown lab files for various topics. Replace 'topic' with a short name of the topic.
The assets directory contains css styles, headers, footers, logos etc. If you are using images in your .Rmd file, place them in the directory images and refer to them using relative path like . Images generated in R during rendering of the .Rmd file is automatically handled. If you have data (tsv, csv, txt text files, .Rds files), place them inside the directory data and read them using relative path x <- read.delim("./data/table.txt"). Do not use paths that link outside of the project environment.
The website is rendered by running rmarkdown::render_site() in the project directory. This generates the HTML files and all other necessary files (including the assets, images and data directories) and moves them into a directory named docs. Open docs/index.html to start. The output directory is set to docs because this GitHub repo uses the docs directory as the Github pages (rendered content) source.
For testing purposes, you can run rmarkdown::render("bla.Rmd") on individual Rmd files. This is a time-saver as the whole website need not be rendered just to preview this one file.
2019 NBIS | SciLifeLab