_config.yml

theme: jekyll-theme-minimal
title: 'Advanced Single Cell RNA-Seq Workshop'
show_downloads: True
google_analytics: True
navigation:
  - title: Home
    url: /

  - heading: Introduction and Lectures
  - title: Intro to the Workshop and Core
    url: base/welcome
  - title: Schedule
    url: base/schedule
  - title: What is Bioinformatics/Genomics?
    url: https://raw.githubusercontent.com/ucdavis-bioinformatics-training/ucdavis-bioinformatics-training.presentations/master/genomics/Genomics_a_perspective_May_2020.pdf
  - title: Experimental Design and Cost Estimation
    url: https://raw.githubusercontent.com/ucdavis-bioinformatics-training/ucdavis-bioinformatics-training.presentations/master/singlecell/scRNAseq-expDesign_May_2020.pdf
  - title: Single Cell Sample Preparation - Dr. Diana Burkart-Waco
    url: https://raw.githubusercontent.com/ucdavis-bioinformatics-training/ucdavis-bioinformatics-training.presentations/master/singlecell/2020_SingleCell_SampleTalk_DBurkart.pdf

  - heading: Support
  - title: Cheat Sheets
    url: base/cheatSheetIndex
  - title: Software and Links
    url: software_scripts/software
  - title: Scripts
    url: software_scripts/scripts_links

  - heading: Prerequisites
  - title: CLI - Logging in and Transferring Files
    url: prerequisites/cli/logging-in
  - title: CLI - Intro to Command-Line
    url: prerequisites/cli/command-line-intro
  - title: CLI - Advanced Command-Line (extra)
    url: prerequisites/cli/advanced-command-line
  - title: CLI - Running jobs on the Cluster and using modules
    url: prerequisites/cli/cluster
  - title: R - Getting Started
    url: prerequisites/intro2R/RStudio
  - title: R - Intro to R
    url: prerequisites/intro2R/Intro2R_fixed
  - title: R - Prepare Data in R (extra)
    url: prerequisites/intro2R/data_in_R_prepare_fixed
  - title: R - Data in R (extra)
    url: prerequisites/intro2R/data_in_R_fixed
  - title: More Materials (extra)
    url: https://ucdavis-bioinformatics-training.github.io/2019-Winter-Bioinformatics_Command_Line_and_R_Prerequisites_Workshop/

  - heading: Data Reduction
  - title: Generating Expression Matrices
    url: data_reduction/Expression_Matrix
  - title: Expression project setup
    url: data_reduction/project_setup_counting
  - title: Preprocessing reads with HTStream
    url: data_reduction/scrna_htstream
  - title: Generating Expression Tables
    url: data_reduction/scMapping
  - title: VDJ T cell and B cell
    url: data_reduction/VDJ
  - title: Velocity analysis
    url:   data_reduction/Velocyto

  - heading: Data analysis
  - title: scRNA analysis prepare
    url: data_analysis/scrna_analysis_prepare
  - title: Mapping Comparison
    url: data_analysis/Mapping_Comparison_fixed
  - title: Anchoring (Comparison dataset)
    url: data_analysis/anchoring_fixed
  - title: Shiny App Install/Overview
    url: data_analysis/shiny_app_install
  - title: App Practical Usage
    url: data_analysis/shiny_practical
  - title: AWS Hosted App (Optional)
    url: data_analysis/shiny_on_aws
  - title: Monocle
    url: data_analysis/adv_scrnaseq_monocle_fixed
  - title: VDJ T cell and B cell analysis
    url: data_analysis/VDJ_Analysis_fixed
  - title: Velocity  analysis
    url:  data_analysis/Velocyto_fixed

  - heading: ETC
  - title: Closing thoughts
    url: base/closing
  - title: Workshop Photos
    url: photos/photos
  - title: Github page
    url: https://github.com/ucdavis-bioinformatics-training/2020-Advanced_Single_Cell_RNA_Seq
  - title: Biocore website
    url: http://bioinformatics.ucdavis.edu