GEN242
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About
Introduction
Syllabus
Schedule
Internal
Resources
Installation
Slides
Course Introduction (S1)
Genome Basics (S2)
Databases and Software (S3)
Git and GitHub (S4)
Linux Cluster Basics (S5)
DNA Sequencing (S6)
Introduction to R (S7)
Sequence Alignments (S8)
Programming in R (S9)
Multiple Alignments (S10)
Short Read Alignments (S11)
R on HPC (S12)
NGS Analysis Basics (S13)
Gene Expression Analysis (S14)
NGS Workflows (S15)
Cluster Analysis (S16)
Enrichment Analysis (S17)
ChIP-Seq Overview (S18)
VAR-Seq Overview (S19)
Project Data (S20)
Graphics in R (S21)
Tidyverse and SQLite (S22)
Building R Packages (S23)
Workflow Review (S24)
CWL (S25)
Final Discussion (S26)
Additional Slide Shows (S27)
Tutorials
GitHub Introduction (T1)
Linux and HPCC Cluster (T2)
Introduction to R (T3)
Programming in R (T4)
Parallel R (T5)
NGS Analysis Basics (T6)
Workflows (T7)
RNA-Seq Workflow (T8)
Cluster Analysis and Data Mining (T9)
Functional Enrichment Analysis (T10)
ChIP-Seq Workflow (T11)
scRNA-Seq Embedding Methods (T11)
VAR-Seq Workflow (T13)
R Markdown (T14)
Project Data (T15)
Graphics and Visualization (T16)
Shiny Apps (T17)
Tidyverse and SQLite (T18)
Building R Packages (T19)
Automate CWL Creation (T20)
Assignments
Homework
HW1: Intro & GitHub
HW2: Linux & HPC
HW3: R Basics
HW4: Alignments
HW5: R Programming
HW6: NGS Analysis Basics
HW7: RNA-Seq Analysis
HW8: R Markdown
Projects
Overview of Projects
RNA-Seq Aligners
DEG Methods
DET Methods
Cluster Analysis
scRNA-Seq Embedding
ChIP-Seq Peak Callers
Functional Enrichment
Motif Enrichment*
Genome Graphics*
Drug-target Analysis
lncRNA Discovery
Variant Callers
Project Data
Presentations
Paper Presentations
Links
Piazza
GitHub Classroom
GitHub Repo
Bioconductor
Hugo, Docsy & R
News
Assignments
Homework
HW1: Intro & GitHub
HW2: Linux & HPC
HW3: R Basics
HW4: Alignments
HW4: Pairwise Alignment Solutions
HW5: R Programming
HW6: NGS Analysis Basics
HW6: RNA-Seq Analysis
HW8: R Markdown
Projects
Overview of Projects
RNA-Seq Aligners
DEG Methods
Cluster Analysis
DEG Methods
scRNA-Seq Embedding
ChIP-Seq Peak Callers
Functional Enrichment
Motif Enrichment
Drug-target analysis
Genome Graphics
lncRNAs and ORFs
Project Data
Variant Callers
Presentations
Paper Presentations
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Create project issue
Assignments
Homework
Homework Assignments
1 minute read
The homework assignments will be posted in this section.
HW1 - Online Exercise and Basic GitHub Usage
HW2 - Introduction to Biocluster and Linux
HW3 - Introduction to R
HW4: Pairwise Alignments
HW4: Pairwise Alignment Solutions
HW5 - Programming in R
HW6 - NGS Analysis Basics
HW7 - RNA-Seq Analysis
HW8 - R Markdown Exercises
Last modified 2025-05-26:
some edits (1747f3b)