Classroom: LeConte 107
| Date | Weekly topic |
Homework |
R code |
Reading
|
| Week Sep 21 |
Syllabus,
Lecture
1: Introduction to R Calendar Lecture 2: Introduction to R and Bioconductor |
Homework 1 Homework Template Rmarkdown cheat sheet |
Applied
Statistics for Bioinformatics Using R ALLpheno.csv Lab1.R |
Chap 1 (Gondro) Chap1 (Krijnen) |
| Week Sep 28 |
R Basic (Lab2.R, Lab3.R) |
Lab2.R Lab3.R Visualization ggplot2 ggplot2 cheat sheet |
Chap2 (Krijnen) Chap3 (Krijnen) |
|
| Week Sep 04 |
Sep 04: Labor Day |
Party in NYC Homework 1 Due (Sep 8 at 5PM) Homework 2 |
Lab4.R |
Chap 4
(Krijnen) Chap 5 (Krijnen) Chap 2 (Gondro) |
| Week Sep 11 |
Guest Lectures: Dr. Shannon Davis Lecture 3: Introduction to Biology I Lecture 4: Introduction to Biology II |
Chap 3 (Gondro) |
||
| Week Sep 18 |
Lecture 5: Review Statistics I Lecture 6: Review Statistics II (Categorical Data, Statistical Models, Regression Analysis) |
Homework 2 Due (Sep 14 at 5PM) Homework 3 |
Lab5.R Lab6.R Lab7.R |
Chap 4 (Gondro) |
| Week Sep 25 |
Lecture 7: Simple Marker Association Test Lecture 7: Simple Marker Association Test Lecture 7 (part II): Additive, Dominant, Codominant, Recessive model |
Final Project Instruction Final Project Proposal Template Homework 3 Due (Sep 28 at 5PM) Homework 4 |
Lab8.R Lab9.R |
Chap 4 (Gondro) |
| Week Oct 02 |
Lecture 8: Genome-wide Association Study Lecture 9: Multiple Comparisons |
Homework 4 Due (October 12 at 5PM) Homework 5 |
Lab10.R |
Chap 5 (Gondro) |
| Week Oct 09 |
Lecture 10: Confounding Effect |
Homework 5 Due (October 26 at 5PM) Homework 6 |
||
Week Oct 16 |
Lecture 11: Introduction to Gene Expression Microarray |
Homework 6 Due (November 2 at 5PM) Homework 7 sampleInfo.txt GSE |
Lab11.R |
Reading List for NGS Chap 3 (Bioconductor) Chap 6 (Krijnen) |
| Week Oct 23 |
Lecture12: Microarray Data Analysis: Preprocessing I Lecture 13: Microarray Data Analysis: Preprocessing II |
Lab12.R Lab13.R |
Chap 6 (Gondro)
Chap 6 (Bioconductor) |
|
| Week Oct 30 |
Lecture 14: Differential Gene Expression Analysis Lecture 15: Differential Gene Expression Analysis Gene Expression Study from Patients with COVID-19 (study 1) Gene Expression Study from Patients with SARS-CoV (study 2) |
Final Project Proposal Due (November 9 at 5PM) Homework 7 Due (November 16 at 5PM) |
Lab14.R Linux Commands Linux File Transfer Lab15.R test.R test.sh |
Chap 6 (Gondro) |
| Week Nov 06 |
Lecture 16: Introduction to Next Generation Sequencing Data Analysis Lecture 17: Next Generation Sequencing Data Analysis: Alignment |
DesignMatrix.R |
||
| Week Nov 13 |
Lecture 18: Differential Expression and Pathway Analysis Using RNAseq data Lecture 19: Gene Set Enrichment Analysis |
Lab16.R Download FASTQ file from SRA RNAseq.fastq rna_1_1.fq.bz2 rna_2_1.fq.bz2 Bowtie and Samtools Lab17.R Lab18.R |
||
| Week Nov 20 |
Lecture 20: Single-Cell RNAseq Data Analysis |
Final Project Template Final Project format |
Link to request account on Bolden (Note: request account for STAT588 on Bolden) UseBolden UseBoldenSubmitJob test.R test.sh |
|
| Week Nov 27 |
Lecture 21: Single-Cell RNAseq Data Analysis II Lecture 22: Single-Cell RNAseq Data Analysis III |
Lab21.R |
||
| Week De 04 |
Lecture23: Single-Cell RNAseq Data Analysis IV | Final
Project Due December 7, Thursday at 5PM (EST) |
Lab22.R |
