_site.yml

name: Analysis of RNA-Seq data
# output directory used on gh-pages branch. format: YYMM
output_dir: 2403
# used site-wide wherever uppmax project ids are used
uppmax_project: g2020006
uppmax_res_1: g2020006_1
# location options are linkoping, lund, umea, uppsala or online
location: uppsala
assistants: 
favicon: assets/favicon.png
exclude: ["docs","README.md","schedule.csv","LICENSE","LICENSE.md","scripts","tmprepo"]
navbar:
  title: '<img src="assets/logo.svg" id="logo" style="height:22px;margin:0;"/>'
  type: default
  logo:
    image: "assets/logo.svg"
    href: https://NBISweden.github.io/workshop-RNAseq
  right:
    - text: Home
      href: index.html
    - text: Schedule
      href: home_schedule.html
    - text: Content
      href: home_content.html
    - text: Precourse
      href: home_precourse.html

# r packages needed for the workshop
# used in home_precourse.Rmd
# split into cran and bioc packages
# if a package is needed by students and repo, add to _student
# if a package is only needed for repo (build, rendering etc), add to _repo
packages:
 packages_cran_student:
  - BiocManager
  - remotes
  - dplyr
  - enrichR
  - ggplot2
  - gridExtra
  - pheatmap
  - pvclust
  - rafalib
  - stringr
  - tidyr
 packages_bioc_student:
  - biomaRt
  - DESeq2
  - edgeR
  - fgsea
  - GEOquery
 packages_github_student:
 packages_cran_repo:
  - bookdown
  - formattable
  - kableExtra
  - knitr
  - leaflet
  - lubridate
  - markdown
  - pagedown
  - rmarkdown
  - xaringan
  - yaml
  - locfit
 packages_bioc_repo:
 packages_github_repo:
  - rstudio/fontawesome