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_config.yml
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theme: jekyll-theme-minimal
title: 'RNA-Seq Analysis'
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_Dec_2021.pdf
- title: Experimental Design and Cost Estimation
url: https://raw.githubusercontent.com/ucdavis-bioinformatics-training/ucdavis-bioinformatics-training.presentations/master/mrna/mRNAseq-expDesign_May_2020.pdf
- title: RNA Sequencing Technologies - Dr. Lutz Froenicke
url: https://raw.githubusercontent.com/ucdavis-bioinformatics-training/ucdavis-bioinformatics-training.presentations/master/mrna/Lutz_Froenicke_RNASeq_2021.pdf
- heading: Support
- title: Zoom
url: base/zoom
- title: Slack
url: base/slack
- 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
url: base/cli_prerequisites
- title: R
url: base/r_prerequisites
- heading: Data Reduction
- title: Files and Filetypes
url: data_reduction/filetypes
- title: Prepare dataset
url: data_reduction/00-project_setup_mm
- title: Preprocessing raw data
url: data_reduction/01-preproc_htstream_mm
- title: Indexing a Genome
url: data_reduction/02-alignment-indexref_mm
- title: Alignment with Star
url: data_reduction/02-alignment_mm
- title: Generating counts tables
url: data_reduction/03-counts_mm
- title: Alignment/Counts with Salmon (Extra)
url: data_reduction/02-salmon_mm
- title: 3' TagSeq
url: data_reduction/02-tagseq_mm
- heading: Data analysis
- title: Prepare R for data analysis
url: data_analysis/de_analysis_prepare_mm
- title: Annotation from BioMart
url: data_analysis/annotation_mm
- title: Differential Expression Analysis
url: data_analysis/DE_Analysis_mm_with_quizzes
- title: Pathway Analysis
url: data_analysis/enrichment_mm_with_quizzes
- title: Comparison between STAR and Salmon
url: data_analysis/compare_star_salmon_mm
- heading: ETC
- title: Closing thoughts
url: base/closing
- title: Workshop Photos
url: photos/photos
- title: Github page
url: https://github.com/ucdavis-bioinformatics-training/2023-June-RNA-Seq-Analysis
- title: Report Errors
url: https://github.com/ucdavis-bioinformatics-training/2023-June-RNA-Seq-Analysis/issues
- title: Biocore website
url: http://bioinformatics.ucdavis.edu