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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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Slides
Short Read Alignments

Short Read Alignments

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To be posted.

Last modified 2022-04-18: some edits (b3bf3fd77)

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