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Overview
Syllabus
Reading
Labs
Computing Resources
Project
FALL 2016
Lectures
Mon 9:30-11:00
Wed 9:30-11:00
Labs
Fri 1:00-4:00
Room
BH-215
Professor
Katie Pollard
TA
Svetlana Lyalina
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Labs
Bring your laptop to all lab sessions.
Homework portion of each lab is due the following Wednesday by
email to Prof. Pollard.
| Date | Topic | Files | To Prepare |
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| 30-Sept | UCSC Genome Browser | Browser Handout
Answer Key | Download: Enhancer predictions from Erwin
et al. (Data File S1)
Homework: Exercises 7, 8, 15, and
16 |
| 7-Oct | Niche modeling of microbial communities | Instructions , Sampling location data, Global environmental data, Code, Homework R
code, Homework Plot |
Download: All Files, unzip FormattedRasters
Confirm: R is
installed
Install: glmulti,
relaimpo
(R packages) |
| 14-Oct | Differential expression with RNA-seq |
Instructions, Expression data, Answer Key
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Download: All files, unzip Instructions and open RNASeq.html
Install: edgeR, pheatmap (R packages)
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| 21-Oct | Machine learning for epigenomics | Repository, Answer Key | Install:
Chrome browser |
| 28-Oct | Population genetics | Code |
Install: msm
(R package)
Review: code from genetics lectures |
| 4-Nov | Cytoscape networks | Files, Answer Key | Confirm:
Java
(JRE 8 u65 or u66) is installed,
Install: plyr,
ggplot2,
RColorBrewer
(R packages),
Cytoscape 3.4
plus apps intallable from inside Cytoscape: PINBPA, BINGO |
| 18-Nov | Protein structure modeling | Tutorial, Slides | Install: IMP,
Chimera, Biopython (sudo easy_install pip; sudo pip install biopython),
scikit-learn (sudo pip install scikit-learn)
If you have anaconda: conda config --add channels salilab;
conda install imp scikit-learn matplotlib biopython
Confirm:
Python packages numpy, scipy, matplotlib are installed |
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