A Class Outlines
These are the specific topics covered in each week.
A.1 Week 1
- Course Intro & Details (slides)
- Assignment 0
- Intro: Data in Biology (slides)
- Prelim: The R Language (slides)
- Prelim: RStudio on SCC (slides)
- Prelim: The R Script (slides)
- Prelim: The Scripting Workflow (slides)
- Comm: RMarkdown & knitr (slides)
- Prelim: Git + github (slides)
- R Prog: R Syntax Basics (slides)
- R Prog: Functions (slides)
- R Prog: Data structures (slides)
- R Prog: Factors (slides)
- R Prog: Iteration (slides)
- R Prog: Troubleshooting and Debugging (slides)
A.2 Week 2
- Assignment 1
- Data Wrangle: The Tidyverse (slides)
- Data Wrangle: Tidyverse Basics (slides)
- Data Wrangle: Importing Data (slides)
- Bioinfo: CSV Files (slides)
- Data Wrangle: The tibble (slides)
- Data Wrangle: pipes (slides)
- Data Wrangle: Arranging Data (slides)
- Data Wrangle: Regular expressions (slides)
- Data Wrangle: Rearranging Data (slides)
- Bioinfo: R in Biology (slides)
- Bioinfo: Types of Biological Data (slides)
- Bioinfo: Bioconductor (slides)
- Bioinfo: Gene Identifiers (slides)
- Bioinfo: Mapping Between Identifier Systems (slides)
A.3 Week 3
- Assignment 1 Review
- Assignment 2
- Data Wrangle: Relational Data (slides)
- Bioinfo: Mapping Homologs (slides)
- Data Viz: Grammar of Graphics
- Data Viz: Plotting One Dimension
- Data Viz: Visualizing Distributions
- R Prog: Unit Testing
- Data Sci: Data Modeling
- Data Sci: A Worked Modeling Example
- Data Sci: Data Summarization
- Data Sci: Linear Models
- Data Sci: Flavors of Linear Models
- Bioinfo: Gene Expression
- Bioinfo: Gene Expression Data in Bioconductor
- Bioinfo: Microarrays
- Bioinfo: Microarray Gene Expression Data
- Bioinfo: Differential Expression: Microarrays (limma)
A.4 Week 4
- Assignment 2 Review
- Assignment 3
- Data Sci: Exploratory Data Analysis
- Data Sci: Principal Component Analysis
- Data Sci: Cluster Analysis
- Data Sci: Hierarchical Clustering
- Data Viz: Heatmaps
- Data Viz: Specifying Heatmap Colors
- Data Viz: Dendrograms
A.5 Week 5
- Assignment 3 Review
- Assignment 4
- Bioinfo: High Throughput Sequencing
- Bioinfo: Count Data
- Bioinfo: RNASeq
- Bioinfo: RNASeq Gene Expression Data
- Bioinfo: Filtering Counts
- Bioinfo: Count Distributions
- Bioinfo: Count Normalization
- Bioinfo: Count Transformation
- Bioinfo: Differential Expression: RNASeq
- Bioinfo: DESeq2/EdgeR
- Bioinfo: limma/voom
- Bioinfo: Gene Set Enrichment Analysis
- Bioinfo: Gene Sets
- Bioinfo: Over-representation Analysis
- Bioinfo: Rank-based Analysis
- Bioinfo: fgsea
A.6 Week 6
- Assignment 4 Review
- Assignment 5
- Data Sci: Statistical Distributions
- Data Sci: Random Variables
- Data Sci: Statistical Distribution Basics
- Data Sci: Distributions in R
- Data Sci: Discrete Distributions
- Data Sci: Continuous Distributions
- Data Sci: Empirical Distributions
- Data Sci: Statistical Tests
- Data Sci: p-values
- Data Sci: [Multiple Hypothesis Testing]
- Data Sci: Statistical power
A.7 Week 7
- Assignment 5 Review
- Assignment 6
- Data Viz: Responsible Plotting
- Data Viz: Human Visual Perception
- Data Viz: Visual Encodings
- Data Viz: Elementary Perceptual Tasks
- Data Viz:
ggplotMechanics - Data Viz: Plotting Two or More Dimensions
- Data Viz: Scatter Plots
- Data Viz: Bubble Plots
- Data Viz: Connected Scatter Plots
- Data Viz: Line Plots
- Data Viz: Parallel Coordinate Plots
- Data Viz: Chord Diagrams and Circos Plots
- Data Viz: How To Use Heatmaps Responsibly
- Data Viz: Multiple Plots
- Data Viz: Facet wrapping
- Data Viz: Publication Ready Plots
- R Prog: Coding Style and Conventions
- R Prog: The
stylerpackage
A.8 Week 8
- Assignment 6 Review
- Assignment 7
- RShiny: Rshiny
- RShiny: Introduction
- RShiny: Application Structure
- RShiny: Reactivity
- RShiny: Publishing
A.9 Week 9
- EngineeRing: Toolification
- EngineeRing: The R Interpreter
- EngineeRing:
Rscript - EngineeRing:
commandArgs() - EngineeRing: Parallel Processing
- EngineeRing: Brief Introduction to Parallelization
- EngineeRing:
applyand Friends Are Pleasingly Parallel - EngineeRing: The
parallelpackage - Assignment 7 Checkin
- EngineeRing: Object Oriented Programming in R
- EngineeRing: Building R Packages
A.10 Week 10
- Bioinfo: Biological Pathways
- Bioinfo: [Gene Regulatory Networks]
- Bioinfo: [Protein-Protein Networks]
- Bioinfo: [WGCNA]
- Assignment 7 Review
- Data Sci: Network Analysis
- Data Viz: Network visualization
A.14 Week 14
- Wrap up & feedback
Abbasi, Amir Ali. 2015. “Diversification of Four Human HOX Gene Clusters by Step-Wise Evolution Rather Than Ancient Whole-Genome Duplications.” Dev. Genes Evol. 225 (6): 353–57.
Box, George E P. 1976. “Science and Statistics.” J. Am. Stat. Assoc. 71 (356): 791–99.
Bruford, Elspeth A, Bryony Braschi, Paul Denny, Tamsin E M Jones, Ruth L Seal, and Susan Tweedie. 2020. “Guidelines for Human Gene Nomenclature.” Nat. Genet. 52 (8): 754–58.
Cleveland, William S, and Robert McGill. 1984. “Graphical Perception: Theory, Experimentation, and Application to the Development of Graphical Methods.” J. Am. Stat. Assoc. 79 (387): 531–54.
Dillies, Marie-Agnès, Andrea Rau, Julie Aubert, Christelle Hennequet-Antier, Marine Jeanmougin, Nicolas Servant, Céline Keime, et al. 2013. “A Comprehensive Evaluation of Normalization Methods for Illumina High-Throughput RNA Sequencing Data Analysis.” Brief. Bioinform. 14 (6): 671–83.
Holley, R W, J Apgar, G A Everett, J T Madison, M Marquisee, S H Merrill, J R Penswick, and A Zamir. 1965. “STRUCTURE OF a RIBONUCLEIC ACID.” Science 147 (3664): 1462–65.
Irizarry, Rafael A, Bridget Hobbs, Francois Collin, Yasmin D Beazer-Barclay, Kristen J Antonellis, Uwe Scherf, and Terence P Speed. 2003. “Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data.” Biostatistics 4 (2): 249–64.
Love, Michael I, Wolfgang Huber, and Simon Anders. 2014. “Moderated Estimation of Fold Change and Dispersion for RNA-seq Data with DESeq2.” Genome Biol. 15 (12): 550.
O’Meara, Caitlin C, Joseph A Wamstad, Rachel A Gladstone, Gregory M Fomovsky, Vincent L Butty, Avanti Shrikumar, Joseph B Gannon, Laurie A Boyer, and Richard T Lee. 2015. “Transcriptional Reversion of Cardiac Myocyte Fate During Mammalian Cardiac Regeneration.” Circ. Res. 116 (5): 804–15.
Ritchie, Matthew E, Belinda Phipson, Di Wu, Yifang Hu, Charity W Law, Wei Shi, and Gordon K Smyth. 2015. “Limma Powers Differential Expression Analyses for RNA-sequencing and Microarray Studies.” Nucleic Acids Res., January, gkv007.
Robinson, Mark D, and Alicia Oshlack. 2010. “A Scaling Normalization Method for Differential Expression Analysis of RNA-seq Data.” Genome Biol. 11 (3): R25.
Shows, T B, C A Alper, D Bootsma, M Dorf, T Douglas, T Huisman, S Kit, et al. 1979. “International System for Human Gene Nomenclature (1979) ISGN (1979).” Cytogenet. Cell Genet. 25 (1-4): 96–116.
St-Pierre, Anne P, Violaine Shikon, and David C Schneider. 2018. “Count Data in Biology-Data Transformation or Model Reformation?” Ecol. Evol. 8 (6): 3077–85.
Zhao, Shanrong, Ying Zhang, Ramya Gamini, Baohong Zhang, and David von Schack. 2018. “Evaluation of Two Main RNA-seq Approaches for Gene Quantification in Clinical RNA Sequencing: polyA+ Selection Versus rRNA Depletion.” Sci. Rep. 8 (1): 4781.