STAT 892-004 Integrative Data Science for Plant Phenomics
Spring 2018
Instructors
- Gota Morota
- Toshihiro Obata
- Harkamal Walia
- Hongfeng Yu
- Chi Zhang
- Qi Zhang
Time and Location
- Tues./Thurs. 11:00 - 12:15pm
- Keim Hall 262
Prerequisites
Course Description
This is a plant phenomics data science course. The main data types include image-based phenomic, genomic, metabolomic, and transcriptomic data. Students will become proficient in the principles, statistical models, and practice of data-driven genome-to-phenome analysis via multi-type data integration; and hands-on experience in data analysis using R and/or Matlab. Successful completion of this course will enable students to process and integrate these diverse data types and build genomic linkages.
Texts and Reading Materials
No specific textbook required for this course. Relevant research papers and documents will be used.
Syllabus
Schedule
Lectures will be delivered using a whiteboard and presentation slides.
- 1/9 (T): Overview of plant phenomics
- 1/11 (R): The NIC Greenhouse Innovation Center tour [WWW]
- 1/16 (T): Introduction to R/RStudio [HTML][GitHub]
- 1/18 (R): Introduction to R/RStudio; Introduction to MATLAB
- 1/23 (T): Pixelomics - Fundamentals [HW1]
- 1/25 (R): Pixelomics - Thresholding; Edge detection
- 1/30 (T): Pixelomics - Spatial filtering; Derived features
- 2/1 (R): Pixelomics - Practices
- 2/6 (T): Genomics - Univariate GWAS [HTML][R]
- 2/8 (R): Genomics - Univariate GWAS
- 2/13 (T): Genomics - Univariate Genomic prediction [HTML][R]
- 2/15 (R): Phenotyping - Introduction to high-throughput phenotyping
- 2/20 (T): Phenotyping - Classical to digital traits [R]
- 2/22 (R): Genomics - Approaches for longitudinal traits [R][P]
- 2/27 (T): Transcriptomics
- 3/1 (R): Transcriptomics
- 3/6 (T): Epigenetics
- 3/8 (R): ChIP-Seq
- 3/13 (T): UNL Plant Breeding Symposium 2018 [WWW]
- 3/15 (R): Gene network
- 3/20 (T): Spring break
- 3/22 (R): Spring break
- 3/27 (T): Gene network
- 3/29 (R): Metabolomics
- 4/3 (T): Metabolomics
- 4/5 (R): Metabolomics
- 4/10 (T): Metabolomics
- 4/12 (R): Data integration [HTML]
- 4/17 (T): Data integration
- 4/19 (R): Student presentations
- 4/24 (T): Student presentations
- 4/26 (R): Student presentations