| Date |
Weekly topic
|
Homework
|
R code
|
Reading
|
Week Aug 19
|
Syllabus
Getting
Started with R and R Studio
R
Markdown (Chapter 20.2 in Rafa)
|
Homework
1
Homework
Template
Rmarkdown
cheat sheet
|
|
Chapter 1 (Irizarry)
Chapter 20 (Irizarry)
Chapter 2 (Irizarry) |
| Week Aug 26 |
Chapter
2: R Basics
Very Basics
Data Types
Vectors
Coercion
Not availables (NA)
Sorting
Vector Arithmetics
Indexing
Basic plots
|
Homework 1 Due
(Aug 30 before class)
Homework
2
|
R-Basics1.R
Link
for Requesting
HPC account
(Choose Research
Computing Account creation)
|
Chapter 3 (Irizarry)
|
Week Sep 02
|
Sep 04: Labor Day
R Basics 2
Getting Data Into R
Getting Results Out of R
Chapter
3: Programming Basics
Conditional Expressions
Defining Functions
Namespaces
For-loops
Vectorized Functions
|
brainbod.txt
brainbod1.txt
brainbod.csv
|
R-Basic2.R
ALLcode.R
programming-basics.R
programming-basics_9_13.R
|
Chapter 4 (Irizarry)
Chapter 5 (Irizarry)
|
Week Sep 09
|
Chapter
3: Programming Basics
Conditional Expressions
Defining Functions
Namespaces
For-loops
Vectorized Functions
|
Homework 2 Due
(Sep 13 before class)
Homework
3
AA.txt
|
RcodeInClass9_9.R
programming_basic_9_18.R
|
Chapter 7 (Irizarry)
Chapter 8 (Irizarry)
|
Week Sep 16
|
Data Visualization
Principles
FlowingData
Data
Exploration Through Time
|
Homework 3 Due
(Sep 27 before class)
Homework
4
|
tidyverse.R
Visualization
ggplot2
ggplot2
cheat sheet
|
Chapter 9 (Irizarry)
Chapter 10 (Irizarry)
|
Week Sep 23
|
Introduction
to RNAseq Methods and Experimental Design
What
is "n" is cell culture experiments?
Confounding
Effect
|
Homework4 Due
(Oct 4 before class)
|
raw-Counts.tsv
experiment-design.tsv
|
|
Week Sep 30
|
RNAseq
Quality Assessment
RNAseq
Alignment
|
Final
Project Instruction
Final
Project Proposal Template
Homework
5
|
Download
FASTQ file from SRA
RNAseq.fastq
rna_1_1.fq.bz2
rna_2_1.fq.bz2
Bowtie and Samtools
RNAseqAlignment.R
RNAseqAlignment2.R
|
|
Week Oct 07
|
Count
normalization with DESeq2
DGE QC
Analysis
|
Homework 5 Due
(Oct 16 before class)
Homework
6
|
DGE_QC.R
DESeq2-Rcode.R
|
|
Week Oct 16
|
Gene-Level
DE Analysis
Gene-Level
DE Analysis II |
Homework 6 Due
(Nov 8 before class)
Homework 7
targets.txt
|
|
Reading List for NGS
Chap 3 (Bioconductor)
Chap 6 (Krijnen)
|
Week Oct 14
|
Multiple Comparisons
Functional Analysis
Differential
Co-Expression Analysis
|
|
FunctionalAnalysis.R
scDECO.R
fast-CoExpress.R
FAST_CoExpress_functions.R
|
Chap 6 (Gondro)
Chap 6 (Bioconductor)
|
Week Oct 21
|
Single-Cell
RNAseq Data Analysis
|
Final Project Proposal Due (November 11 Before Class)
Homework 7 Due
(November 16 at 5PM)
|
HPC
tutorial
Linux
Commands
Linux
File Transfer
test.R
test.sh
|
Chap 6 (Gondro)
|
Week Oct 28
|
Single-Cell
RNAseq Data Analysis II
|
|
scRNAseq
data dropbox link
SC2.R
|
|
Week Nov 04
|
Single-Cell
RNAseq Data Analysis III
|
|
SC3.R
scNormalization.R
|
|
Week Nov 11
|
Single-Cell
RNAseq Data Analysis IV
|
Final Project Template
Final Project
format
|
SC4.R
SCimmune.R
|
|
Week Nov 18
|
Student Presentation
|
|
|
|
Week De 02
|
Student Presentation |
Final
Project Due
December 11, 2024 Wed before 5PM
(EST)
|
|
|
