This site contains course materials, scripts, homeworks, and resources for Computational Biology, Spring 2017.
Lecture Outlines, R-Scripts, & Homework Assignments
| Date | Lecture | Scripts | Homework |
|---|---|---|---|
| January 17 | GitHub | - | - |
| January 18 | - | - | Homework #1 |
| January 19 | Thinking On Paper | - | - |
| January 24 | RStudio | - | - |
| January 25 | - | - | Homework #2 |
| January 26 | RStudio II | - | - |
| January 31 | Beamer Slides | R-Scripts | - |
| February 1 | - | - | Homework #3 |
| February 2 | Importing Data | R-Scripts | - |
| February 7 | Regular Expressions | R-Scripts | - |
| February 8 | - | - | Homework #4 |
| February 9 | Regular Expressions II | R-Scripts | - |
| February 14 | Atomic Vectors | R-Scripts | - |
| February 15 | - | - | Homework #5 |
| February 16 | Data Structures | - | - |
| February 21 | Subsetting | - | - |
| February 22 | - | - | Homework #6 |
| February 23 | Probability Distributions | - | - |
| February 28 | Probability Distributions II | - | - |
| March 1 | - | - | Homework #7 |
| March 2 | Functions | - | - |
| March 7 | TOWN MEETING DAY RECESS | - | - |
| March 8 | - | - | Homework #8 |
| March 9 | Structured Programming | R-Scripts | - |
| March 14 | SPRING RECESS | - | - |
| March 15 | SPRING RECESS | - | - |
| March 16 | SPRING RECESS | - | - |
| March 21 | Guest Lecture: Dr. Brandon Ogbunugafor | - | - |
| March 22 | - | - | Homework #9 |
| March 23 | NO CLASS | - | - |
| March 28 | Control Structures | - | - |
| March 29 | - | - | Catch-up Day |
| March 30 | Control Structures II | - | - |
| April 4 | Control Structures III | - | - |
| April 5 | - | - | Homework #10 |
| April 6 | Control Structures IV | - | - |
| April 11 | Randomization Tests | - | - |
| April 12 | - | - | Spatial Analysis |
| April 13 | Markov Models | - | - |
| April 18 | Markov Models II | - | - |
| April 19 | - | - | R Presentations: Garrett, Mikucki, Southgate, Kazenal |
| April 20 | Apply Functions | - | - |
| April 25 | Base Graphics I | - | - |
| April 26 | - | - | R Presentations: Nevins, Clark, Keller, Looi |
| April 27 | Base Graphics II | - | - |
| May 2 | Research Presentations: Clark, Southgate, Keller, Looi | - | - |
| May 3 | - | - | R Presentations: Alger, Burnham, Ashlock; Research Presentations: Nevins, Garrett, Kazenal |
| May 4 | Research Presentations: Alger, Mikucki, Burnham, Ashlock | - | - |
Class Work
| Student | Fun Fact |
|---|---|
| Samantha Alger GitHub Portfolio | I am a beekeeper. |
| Lauren Ash GitHub Portfolio | While interning at Busch Gardens in Florida, I made friends with Rosie the elephant because she would sway and stare at me for hours. |
| Lauren Ashlock GitHub Portfolio | I have a 13 year old cockatiel named Rosie. |
| Alex Burnham GitHub Portfolio | I used to own a business called “Burnham Custom Amplification” where I hand built boutique custom speaker cabinets for guitar and bass players. |
| Peter Clark GitHub Portfolio | I enjoy plants that grow on cliffs. |
| April Garrett GitHub Portfolio | As a reward for getting through Comps at the end of this semester, I plan to enroll in River Dancing classes in Colchester starting this summer. |
| Nick Gotelli GitHub Portfolio | For 33 years, I have raised pure-bred, show-quality chow chows. |
| Melanie Kazenal GitHub Portfolio | After completing my undergraduate degree, I worked for two years as an immigration law paralegal. |
| Erin Keller GitHub Portfolio | I can speak Norwegian! Jeg kan snakker norsk! |
| Alex Looi GitHub Portfolio | I like to run, a lot, and I have a personal running coach who lives in San Fran. |
| Emily Mickuki GitHub Portfolio | I have scars on my arm from being bitten by a sloth! |
| Matthias Nevins GitHub Portfolio | I was home-schooled until 8th grade. |
| Morgan Southgate GitHub Portfolio | Over this winter break, I attended Dave Barrington’s Tropical Plant Systematics field course in Costa Rica. |
Class R Presentations
| Author | Title |
|---|---|
| Samantha Alger | Spatial Mapping With tmap |
| Lauren Ash | Spatial Analysis With ggmap |
| Lauren Ashlock | RNA-Seq Analysis With DESEQ2 |
| Alex Burnham | Improved Graphics With ggplot |
| Peter Clark | Biodiversity Metrics With vegan |
| April Garrett | SNP Data analysis with bioconductor |
| Melanie Kazenal | Data Wrangling With plyr |
| Erin Keller | Interactive Web Pages With shiny |
| Alex Looi | Data Scraping From The Web With Custom Functions |
| Emily Mikucki | Animated Graphics With animation |
| Matthias Nevins | Random Forest Trees With randomForest |
| Morgan Southgate | Null Model Analysis With EcoSimR |