GEN242
  • 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
  • Slides
    • Course Introduction Genome Basics Databases and Software Git and GitHub Linux and Cluster Basics 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 Cluster Analysis Functional Enrichment Analysis ChIP-Seq Analysis VAR-Seq Analysis Project Data R Graphics R packages dplyr, tidyr and SQLite Review of Data Analysis Workflows Structure and Auto-Generation of CWL Parameter Files Additional Slide Shows Final Discussion
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  1. Slides

Slides

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Course Introduction

Genome Basics

Databases and Software

Git and GitHub

Linux and HPC Cluster Basics

Sequencing Technologies

Introduction to R

Sequence Alignments and Similarity Searching

Programming in R

Multiple Alignments

Short Read Alignments

R on HPC Systems

NGS Analysis Basics

Analysis of Gene Expression Data

Introduction to NGS Workflows

Cluster Analysis

Functional Enrichment Analysis

ChIP-Seq Analysis

VAR-Seq Analysis

Project Data Management

Graphics and Data Visualization in R

Building R packages

Tidyverse and Some SQLite

Review of Data Analysis Workflows

Structure and Auto-Generation of CWL Parameter Files

Additional Slide Shows

Final Discussion

Last modified 2022-03-21: some edits (76115cf94)
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