GEN242-2021
  • 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) More on Workflows (S21) Additional Slide Shows (S22)
  • 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 Cluster Analysis scRNA-Seq Embedding ChIP-Seq Peak Callers Functional Enrichment Motif Enrichment Genome Graphics 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 scRNA-Seq Embedding ChIP-Seq Peak Callers Functional Enrichment Motif Enrichment Genome Graphics Project Data
      • Presentations
        • Paper Presentations
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  1. Assignments
  2. Projects

Projects

1 minute read

Projects will be posted here.


Overview of Course Projects

RNA-Seq - NGS Aligners

RNA-Seq - DEG Analysis Methods

Cluster and Network Analysis Methods

Embedding Methods for scRNA-Seq

ChIP-Seq Peak Callers

Functional enrichment analysis (FEA)

Motif Enrichment Analysis (MEA)

Genome Summary Graphics

Data Management for Course Projects

Last modified 2022-03-14: some edits (ee391e1d8)
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