1 Detailed Class Schedule
1.1 Week 1
| Lecture | Topic | Section | Slides |
|---|---|---|---|
| 1 | Intro | [Course Intro & Details] | |
| 1 | Assignment | Assignment 0 | |
| 1 | Intro | Data in Biology | slides |
| 1 | Prelim | The R Language | slides |
| 1 | Prelim | Rstudio | slides |
| 1 | Prelim | The R Script | slides |
| 1 | Prelim | The Scripting Workflow | slides |
| 1 | Comm | Rmarkdown & knitr | slides |
| 1 | Prelim | Git + github | slides |
| 1 | R Prog | R Syntax Basics | slides |
| 1 | R Prog | Data Structures | slides |
| 1 | R Prog | [Subsetting Data Structures] | slides |
| 2 | R Prog | Logical Tests and Comparators | slides |
| 2 | R Prog | Functions | slides |
| 2 | R Prog | Factors | slides |
| 2 | R Prog | Iteration | slides |
| 2 | R Prog | Troubleshooting and Debugging | slides |
1.2 Week 2
| Lecture | Topic | Section | Slides |
|---|---|---|---|
| 3 | EngineeRing | Unit Testing | slides |
| 3 | Intro | [Assignment Structure] | slides |
| 3 | Assignment | [Assignment 1 - Base R] | |
| 3 | Data Wrangling | The Tidyverse | slides |
| 3 | Data Wrangling | Tidyverse Basics | slides |
| 3 | Data Wrangling | Importing Data | slides |
| 3 | Bioinfo | CSV Files | slides |
| 3 | Data Wrangling | The tibble | slides |
| 3 | Data Wrangling | pipes | slides |
| 3 | Data Wrangling | Arranging Data | slides |
| 3 | Data Wrangling | Regular expressions | slides |
| 4 | Data Wrangling | Grouping Data | slides |
| 4 | Data Wrangling | Rearranging Data | slides |
1.3 Week 3
| Lecture | Topic | Section | Slides |
|---|---|---|---|
| 5 | Assignment | [Assignment 1 - Base R] | |
| 5 | R Prog | Installing Packages | slides |
| 5 | Assignment | [Assignment 2 - Tidyverse Basics] | |
| 5 | Bioinfo | R in Biology | slides |
| 5 | Bioinfo | Types of Biological Data | slides |
| 5 | Bioinfo | Bioconductor | slides |
| 5 | Bioinfo | Gene Identifiers | slides |
| 5 | Bioinfo | Mapping Between Identifier Systems | slides |
| 6 | Data Wrangling | Relational Data | slides |
| 6 | Bioinfo | Mapping Homologs | slides |
1.4 Week 4
| Lecture | Topic | Section | Slides |
|---|---|---|---|
| 7 | Assignment | [Assignment 2 - Tidyverse Basics] | |
| 7 | Assignment | [Assignment 3 - Bioinformatics Basics] | |
| 7 | Bioinfo | Gene Expression | slides |
| 7 | Bioinfo | Gene Expression Data in Bioconductor | slides |
| 7 | Bioinfo | Microarrays | slides |
| 7 | Bioinfo | Microarray Gene Expression Data | slides |
| 8 | Data Viz | Grammar of Graphics | slides |
| 8 | Data Viz | ggplot Mechanics |
slides |
| 8 | Data Viz | Plotting One Dimension | slides |
| 8 | Data Viz | Visualizing Distributions | slides |
1.5 Week 5
| Lecture | Topic | Section | Slides |
|---|---|---|---|
| 9 | Assignment | [Assignment 3 - Bioinformatics Basics] | |
| 9 | Assignment | [Assignment 4 - Data Science Basics] | |
| 9 | Data Science | Data Modeling | slides |
| 9 | Data Science | A Worked Modeling Example | slides |
| 9 | Data Science | Exploratory Data Analysis | slides |
| 9 | Data Science | Principal Component Analysis | slides |
| 10 | Data Viz | Heatmaps | slides |
| 10 | Data Science | Data Summarization | slides |
| 10 | Data Science | Linear Models | slides |
| 10 | Data Science | Flavors of Linear Models | slides |
| 10 | Data Science | Cluster Analysis | slides |
| 10 | Data Science | Hierarchical Clustering | slides |
| 10 | Data Viz | Dendrograms | slides |
1.6 Week 6
| Lecture | Topic | Section | Slides |
|---|---|---|---|
| 11 | Assignment | [Assignment 4 - Data Science Basics] | |
| 11 | Assignment | [Assignment 5 - Counts Data] | |
| 11 | Bioinfo | High Throughput Sequencing | slides |
| 11 | Bioinfo | Count Data | slides |
| 11 | Bioinfo | RNASeq | slides |
| 11 | Bioinfo | RNASeq Gene Expression Data | slides |
| 11 | Bioinfo | Filtering Counts | slides |
| 11 | Bioinfo | Count Distributions | slides |
| 11 | Bioinfo | Count Normalization | slides |
| 11 | Bioinfo | Count Transformation | slides |
| 12 | Bioinfo | Differential Expression | slides |
| 12 | Bioinfo | Differential Expression: Microarrays (limma) | slides |
| 12 | Bioinfo | Differential Expression: RNASeq | slides |
| 12 | Bioinfo | DESeq2/EdgeR | slides |
| 12 | Bioinfo | limma/voom | slides |
1.7 Week 7
| Lecture | Topic | Section | Slides |
|---|---|---|---|
| 13 | Assignment | [Assignment 5 - Counts Data] | |
| 13 | Assignment | [Assignment 6 - Differential Expression Part 1] | |
| 13 | Bioinfo | Gene Set Enrichment Analysis | slides |
| 13 | Bioinfo | [Gene Sets] | slides |
| 13 | Bioinfo | [Over-representation Analysis] | slides |
| 13 | Bioinfo | [Rank-based Analysis] | slides |
| 13 | Bioinfo | [fgsea] | slides |
| 14 | Data Science | Statistical Distributions | slides |
| 14 | Data Science | Random Variables | slides |
| 14 | Data Science | [Statistical Distributions Basics] | slides |
| 14 | Data Science | Distributions in R | slides |
| 14 | Data Science | Discrete Distributions | slides |
| 14 | Data Science | Continuous Distributions | slides |
| 14 | Data Science | Empirical Distributions | slides |
1.8 Week 8
| Lecture | Topic | Section | Slides |
|---|---|---|---|
| 15 | Assignment | [Assignment 6 - Differential Expression Part 1] | |
| 15 | Assignment | [Assignment 7 - Differential Expression Part 2] | |
| 15 | Data Viz | Responsible Plotting | slides |
| 15 | Data Viz | Human Visual Perception | slides |
| 15 | Data Viz | Visual Encodings | slides |
| 15 | Data Viz | Elementary Perceptual Tasks | slides |
| 15 | Data Viz | Plotting Two or More Dimensions | slides |
| 15 | Data Viz | Scatter Plots | slides |
| 15 | Data Viz | Bubble Plots | slides |
| 15 | Data Viz | Connected Scatter Plots | slides |
| 15 | Data Viz | Line Plots | slides |
| 16 | Data Viz | Parallel Coordinate Plots | slides |
| 16 | Data Viz | Chord Diagrams and Circos Plots | slides |
| 16 | Data Viz | How To Use Heatmaps Responsibly | slides |
| 16 | Data Viz | Specifying Heatmap Colors | slides |
| 16 | Data Viz | Multiple Plots | slides |
| 16 | Data Viz | Facet wrapping | slides |
| 16 | Data Viz | Publication Ready Plots | slides |
1.9 Week 9
| Lecture | Topic | Section | Slides |
|---|---|---|---|
| 17 | Assignment | [Assignment 7 - Differential Expression Part 2] | |
| 17 | Assignment | [Assignment 8 - RShiny MkI] | |
| 17 | R Prog | Coding Style and Conventions | |
| 17 | R Prog | The styler package |
|
| 17 | RShiny | Rshiny | |
| 17 | RShiny | Introduction | |
| 17 | RShiny | Application Structure | |
| 17 | RShiny | Reactivity | |
| 17 | RShiny | Publishing |
1.10 Week 10
| Lecture | Topic | Section | Slides |
|---|---|---|---|
| 19 | R Prog | [Saving and Loading R Objects] | slides |
| 19 | EngineeRing | Toolification | slides |
| 19 | EngineeRing | The R Interpreter | slides |
| 19 | EngineeRing | Rscript |
slides |
| 19 | EngineeRing | commandArgs() |
slides |
| 19 | EngineeRing | Parallel Processing | slides |
| 19 | EngineeRing | Brief Introduction to Parallelization | slides |
| 19 | EngineeRing | apply and Friends Are Pleasingly Parallel |
slides |
| 19 | EngineeRing | The parallel package |
slides |
| 19 | EngineeRing | Object Oriented Programming in R | slides |
| 20 | EngineeRing | Building R Packages |
1.11 Week 11
| Lecture | Topic | Section | Slides |
|---|---|---|---|
| 21 | Bioinfo | Biological Pathways | |
| 21 | Bioinfo | [Gene Regulatory Networks] | |
| 21 | Bioinfo | [Protein-Protein Networks] | |
| 21 | Bioinfo | [WGCNA] | |
| 22 | Assignment | [Assignment 7] | |
| 22 | Assignment | Final Project | |
| 22 | Data Science | Network Analysis | |
| 22 | Data Viz | Network visualization |
1.12 Week 12
| Lecture | Topic | Section | Slides |
|---|---|---|---|
| 23 | Professional Development | NA | |
| 24 | Professional Development | NA |
1.13 Week 13
| Lecture | Topic | Section | Slides |
|---|---|---|---|
| 25 | Professional Development | NA | |
| 26 | Professional Development | NA |
1.15 Week 15
| Lecture | Topic | Section | Slides |
|---|---|---|---|
| 28 | Orphans, topics without a home. Or parents. | NA | |
| 28 | Data Science | Statistical Tests | slides |
| 28 | Data Science | p-values | slides |
| 28 | Data Science | [Multiple Hypothesis Testing] | slides |
| 28 | Data Science | Statistical power | slides |
[[1]] NULL
[[2]] NULL
[[3]] NULL
[[4]] NULL
[[5]] NULL
[[6]] NULL
[[7]] NULL
[[8]] NULL
[[9]] NULL
[[10]] NULL
[[11]] NULL
[[12]] NULL
[[13]] NULL
[[14]] NULL
[[15]] NULL