GEN242
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About
Introduction
Syllabus
Schedule
Internal
Resources
Installation
Slides
Course Introduction (S1)
Genome Basics (S2)
Databases and Software (S3)
DNA Sequencing (S4)
Introduction to R (S5)
Sequence Alignments (S6)
Programming in R (S7)
Multiple Alignments (S8)
Short Read Alignments (S9)
R on HPC (S10)
NGS Analysis Basics (S11)
Gene Expression Analysis (S12)
NGS Workflows (S13)
ChIP-Seq Overview (S14)
Enrichment Analysis (S15)
Cluster Analysis (S16)
Project Data (S17)
Graphics in R (S18)
Building R Packages (S19)
dplyr, tidyr and SQLite (S20)
Workflow Review (S21)
Final Discussion (S22)
Additional Slide Shows (S23)
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)
ChIP-Seq Workflow (T9)
scRNA-Seq Embedding Methods (T10)
R Markdown (T11)
Functional Enrichment Analysis (T12)
Cluster Analysis and Data Mining (T13)
Project Data (T14)
Graphics and Visualization (T15)
Shiny Apps (T16)
Building R Packages (T17)
dplyr, tidyr and SQLite (T18)
Automate CWL Creation (T19)
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
DEXseq Analysis
Cluster Analysis
scRNA-Seq Embedding
ChIP-Seq Peak Callers
Functional Enrichment
Motif Enrichment*
Genome Graphics*
Drug-target Analysis
lncRNA Discovery
Project Data
Presentations
Paper Presentations
Links
Piazza
GitHub Classroom
GitHub Repo
Bioconductor
Hugo, Docsy & R
News
Slides
Course Introduction
Genome Basics
Databases and Software
DNA Sequencing
Introduction to R
Sequence Alignments
Programming in R
Multiple Alignments
Short Read Alignments
R on HPC
NGS Analysis Basics
Analysis of Gene Expression Data
Introduction to NGS Workflows
ChIP-Seq Overview
Functional Enrichment Analysis
Cluster Analysis
Project Data
R Graphics
R packages
dplyr, tidyr and SQLite
Review of Data Analysis Workflows
Final Discussion
Additional Slide Shows
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Create project issue
Slides
Introduction to NGS Workflows
Introduction to NGS Workflows
1 minute read
To be posted.
Last modified 2022-04-25:
some edits (69ac9cd8d)