v1911

LICENSE

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+MIT License
+
+Copyright (c) 2019 NBIS -- National Bioinformatics Infrastructure Sweden
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+# course_rnaseq
+
+This repo contains the course material for NBIS course **Workshop on RNA-Seq**. The rendered view of this repo is available [here](https://nbisweden.github.io/course_rnaseq/).
+
+## Contributing
+
+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.
+
+## Descriptions
+
+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.  
+
+## Dependencies
+
+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/image.jpg)`. 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.
+
+## Rendering
+
+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
+# rnaseq_201911

_site.yml

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+name: Workshop on RNA-Seq
+favicon: assets/favicon.png
+output_dir: docs
+exclude: ["data","docs","README.md","schedule.csv","LICENSE"]
+navbar:
+  title: "<b>NBIS • Workshop on RNA-Seq</b>"
+  logo:
+    image: "assets/logo-white.svg"
+    href: https://nbisweden.github.io/course_rnaseq
+  right:
+    - text: Home
+      icon: fa-home
+      href: index.html
+    - text: Schedule
+      icon: fa-clipboard-list
+      href: schedule.html
+    - text: Lab
+      icon: fa-flask
+      href: lab.html
+    - text: Precourse
+      icon: fa-pencil-alt
+      href: precourse.html
+    - text: Info
+      icon: fa-info
+      href: info.html
+output:
+  bookdown::html_document2:
+    theme: flatly
+    highlight: tango
+    df_print: default
+    code_folding: none
+    self_contained: false
+    keep_md: false
+    encoding: 'UTF-8'
+    css: "assets/lab.css"
+    include:
+      after_body: assets/footer-lab.html

assets/footer-lab.Rmd

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+
+<hr/>
+
+<div>
+<span style="float:left; vertical-align:middle">
+<b>2019</b> [NBIS](https://nbis.se/) • [SciLifeLab](https://www.scilifelab.se/)
+</span>
+<span style="float:right; vertical-align:middle">
+<span class="footericon" style="padding-right:4px; padding-left:4px">
+<a href="https://nbis.se/"><i class="fas fa-globe-americas"></i></a>
+</span>
+<span class="footericon" style="padding-right:4px; padding-left:4px">
+<a href="https://twitter.com/NBISwe"><i class="fab fa-twitter"></i></a>
+</span>
+<span class="footericon" style="padding-left:4px">
+<a href="https://www.linkedin.com/company/nbisweden/"><i class="fab fa-linkedin"></i></a>
+</span>
+</span>
+</div>

assets/footer-lab.html

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+
+<div class="footer">
+<div class="container" style="padding-top:5px;padding-bottom:5px;">
+<p>
+<span style="float:left; vertical-align:middle">
+<b>2019 </b><a href="https://nbis.se/">NBIS</a> • <a href="https://www.scilifelab.se/">SciLifeLab</a>
+</span>
+<span style="float:right; vertical-align:middle">
+<span class="footericon" style="padding-right:4px; padding-left:4px">
+<a href="https://nbis.se/"><i class="fas fa-globe-americas"></i></a>
+</span>
+<span class="footericon" style="padding-right:4px; padding-left:4px">
+<a href="https://twitter.com/NBISwe"><i class="fab fa-twitter"></i></a>
+</span>
+<span class="footericon" style="padding-left:4px">
+<a href="https://www.linkedin.com/company/nbisweden/"><i class="fab fa-linkedin"></i></a>
+</span>
+</span>
+</p>
+</div>
+</div>

assets/footer-presentation.Rmd

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+
+.end-text[
+`r   x <- sessionInfo(); paste0("<p>",x$R.version$version.string,"<br>","<p>Platform: ",x$platform,"</p>","<p>OS: ",x$running,"</p><br>")`
+
+<hr>
+
+<span class="small">`r paste0("Built on : <i class='fa fa-calendar' aria-hidden='true'></i> ",format(Sys.time(),format='%d-%b-%Y')," at <i class='fa fa-clock-o' aria-hidden='true'></i> ",format(Sys.time(),format='%X'))`</span>  
+
+<b>`r format(Sys.time(), '%Y')`</b> • [SciLifeLab](https://www.scilifelab.se/) • [NBIS](https://nbis.se/)
+]

assets/header-lab.Rmd

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+<!-- rmd lab header -->
+
+<!-- custom fonts -->
+<link href="https://fonts.googleapis.com/css?family=Roboto|Source+Sans+Pro:300,400,600|Ubuntu+Mono&amp;subset=latin-ext" rel="stylesheet">
+
+```{r,include=FALSE,cache=FALSE}
+# load libraries
+library(knitr) # runs pandoc
+library(bookdown) # for markdown
+library(captioner) # for table and figure captions
+```
+
+```{r,include=FALSE,cache=FALSE}
+# prepare captions
+tc <- captioner::captioner(prefix="<b>Tab. </b>")
+fc <- captioner::captioner(prefix="<b>Fig. </b>")
+# knitr options
+knitr::opts_knit$set(progress=TRUE,verbose=TRUE)
+knitr::opts_chunk$set(dev="svg",results="hold",fig.show="hold",fig.align="left",
+                      echo=TRUE,warning=FALSE,message=FALSE,accordion=NULL,
+                      block.title=TRUE)
+```
+
+```{r,include=FALSE,cache=FALSE}
+# custom hooks
+## collapsible panel
+knitr::knit_hooks$set(accordion=function(before,options,envir) {
+  if(before) {
+    id <- paste0("acc",format(Sys.time(),"%Y%m%d%H%S"),sample(c(0:9),1),sample(c(0:9),1),sample(c(0:9),1),sample(c(0:9),1))
+    if(is.null(options$btntype)) {btntype <- "normal"}else{btntype <- options$btntype}
+    paste0('<p>',
+          '<button class="btn btn-sm btn-primary btn-collapse btn-collapse-',btntype,' collapsed" type="button" data-toggle="collapse" data-target="#',id,'" aria-expanded="false" aria-controls="',id,'">',
+          '</button>',
+          '</p>',
+          '<div class="collapse" id="',id,'">',
+          '<div class="card card-body">')
+  }else{
+    paste0("</div>","</div>")
+  }
+})
+
+## show title for code
+knitr::knit_hooks$set(block.title=function(before,options,envir) {
+
+out_class <- NULL
+if(is.null(options$class.output)) {
+if(options$echo) out_class <- options$engine
+if((!options$echo) & (options$results != "hide")) out_class <- "Output"
+}else{
+  out_class <- options$class.output
+}
+
+  if(before) {
+    paste0('<div class="block-title-parent"><div class="block-title small">',out_class,'</div>')
+  }else{
+    paste0('</div>')
+  }
+})
+```
+
+<br>

assets/header-presentation.Rmd

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+<link href="https://fonts.googleapis.com/css?family=Roboto|Source+Sans+Pro:300,400,600|Ubuntu+Mono&amp;subset=latin-ext" rel="stylesheet">
+<link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.3.1/css/all.css" integrity="sha384-mzrmE5qonljUremFsqc01SB46JvROS7bZs3IO2EmfFsd15uHvIt+Y8vEf7N7fWAU" crossorigin="anonymous">
+
+```{r,include=FALSE,eval=knitr::opts_knit$get("rmarkdown.pandoc.to")=="html"}
+# Enables Font Awesome in HTML based bookdown outputs.
+fa <- rmarkdown::html_dependency_font_awesome()
+fa$attachment <- "fonts/fontawesome-webfont.ttf"
+htmltools::tagList(fa)
+```
+
+```{r,echo=FALSE,message=FALSE,warning=FALSE,results='hide'}
+# run setup code
+
+# load libraries
+library(knitr) # runs pandoc
+library(bookdown) # for markdown
+
+# knitr options
+knitr::opts_knit$set(progress=TRUE,verbose=TRUE)
+knitr::opts_chunk$set(dev="svg",results="hold",fig.show="hold",fig.align="left",echo=TRUE,warning=FALSE,message=FALSE)
+```