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2016 CSHL Course - Plant Sciences
CSHL
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R on CRAN
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Girke Lab
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RNA-Seq
Overview
Background
Requirements
Slides
Slides
Introduction to R
1. Overview
2. R Package Repositories
3. Installation of R and Add-on Packages
4. Getting Around
5. Basic Syntax
6. Data Types
7. Data objects
8. Important Utilities
9. Operators and Calculations
10. Reading and Writing External Data
11. Useful R Functions
12. SQLite Databases
13. R Markdown
14. Session Info
15. References
R Graphics
1. Overview
2. Base Graphics
3. Grid Graphics
4. lattice Graphics
5. ggplot2 Graphics
6. Specialty Graphics
7. Genome Graphics
8. References
NGS Workflow Overview
1. Background
2. Getting Started
3. More detail
4. Workflow demo
5. Version information
6. References
RNA-Seq Workflow
1. Introduction
2. Sample definitions and environment settings
3. Read preprocessing
4. Alignments
5. Read distribution across genomic features
6. Read quantification per annotation range
7. Analysis of differentially expressed genes with edgeR
8. GO term enrichment analysis of DEGs
9. Clustering and heat maps
10. Render report in HTML and PDF format
11. Version Information
12. Funding
13. References
R Package Repositories
CRAN (>8,000 packages) general data analysis -
URL
Bioconductor (>1,100 packages) bioscience data analysis -
URL
Omegahat (>90 packages) programming interfaces -
URL