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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) ChIP-Seq Overview (S16) Enrichment Analysis (S17) Cluster Analysis (S18) Project Data (S19) Graphics in R (S20) Building R Packages (S21) dplyr, tidyr and SQLite (S22) Workflow Review (S23) Final Discussion (S24) Additional Slide Shows (S25)
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 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 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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Slides
NGS Analysis Basics

NGS Analysis Basics

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Last modified 2023-04-27: some edits (59df43de0)

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