Schedule is subject to change (but not the exam dates)
| Day & Time | Date | Topic | Reference |
|---|---|---|---|
| Tue 1:10 - 5:00 | 4-Apr | JetStream; Markdown; Intro Linux | Buffalo: p. 1 - 54 (Chapters 1-3) |
| Thur 1:10 - 5:00 | 6-Apr | Intro Linux Continued; Git | Buffalo: p. 67 - 97 (Chapter 5); 125 - 165 (Chapter 7) |
| Fri 1:10 - 2:00 | 7-Apr | Discussion: Linux, Git | |
| Tue 1:10 - 5:00 | 11-Apr | For Loops; BLAST | Chapter 6 of Bioinformatics for Beginners |
| Thur 1:10 - 5:00 | 13-Apr | BLAST continued | |
| Fri 1:10 - 2:00 | 14-Apr | Discussion: For loops, BLAST | |
| Tue 1:10 - 5:00 | 18-Apr | R: Intro | Buffalo: p. 175 - 206 (Start of Chapter 8 to Exploring Data Visually with ggplot2 1: Scatterplots and Densities); R for data science Chapters 27, 4 |
| Thur 1:10 - 5:00 | 20-Apr | R: Tidyverse | R for data science Chapters 5, 6, 10, 18 |
| Fri 1:10 - 2:00 | 21-Apr | Discussion: R, | |
| Tue 1:10 - 5:00 | 25-Apr |
| Thur 1:10 - 5:00 | 27-Apr | Multiple Sequence Alignment and Tree Building | Chapter 9 of Bioinformatics for Beginners |
| Fri 1:10 - 2:00 | 28-Apr | Discussion: Tidyverse, trees, etc | |
| Tue 1:10 - 5:00 | 2-May | R SNPS; ggplot | Buffalo: p. 207 - 224 (Chapter 8 Exploring Data Visually with ggplot2 1: Scatterplots and Densities to Using ggplot2 Facets); R for data science Chapters 3, 12 |
| Thur 1:10 - 5:00 | 4-May | GWAS | Wikipedia GWAS GWAS Q & A GWAS protocol |
| Fri 1:10 - 2:00 | 5-May | Midterm Posted | |
| Tue 1:10 - 5:00 | 9-May | Work on midterm | |
| Thur 1:10 - 5:00 | 11-May | Shiny Midterm Due @ 1:10 |
|
| Fri 1:10 - 2:00 | 12-May | Continue Shiny | |
| Tue 1:10 - 5:00 | 16-May | Illumina Sequence Data: QC and mapping | Buffalo: p. 339 - 351 (Start of Chapter 10 to Indexed FASTA Files) Wikipedia FastQ U Mich SAM wiki |
| Thur 1:10 - 5:00 | 18-May | Illumina: SNPs and IGV | Buffalo p. 355 - 377 (Start of Chapter 11 to Pileups with samtools pileup) |
| Fri 1:10 - 2:00 | 19-May | Discussion: Illumina, etc | |
| Tue 1:10 - 5:00 | 23-May | Illumina: RNAseq | |
| Thur 1:10 - 5:00 | 25-May | Illumina: RNAseq | |
| Fri 1:10 - 2:00 | 26-May | Discussion: RNAseq, etc | |
| Tue 1:10 - 5:00 | 30-May | Motif discovery | |
| Thur 1:10 - 5:00 | 1-Jun | Clustering | |
| Fri 1:10 - 2:00 | 2-Jun | Discussion: Genetic Networks | |
| Tue 1:10 - 5:00 | 6-Jun | Networks | |
| Thur 1:10 - 5:00 | 8-Jun | Metagenomics | |
| Fri | 9-Jun | Final Exam available | |
| Wed 9:00 AM | 14-Jun | Final Exam Due 9AM |