sidebar

toc

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

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 Workflows Additional Slide Shows

View source code Edit this page Create child page Create documentation issue Create project issue

Slides
Short Read Alignments

Short Read Alignments

1 minute read

Last modified 2021-04-20: some edits (89d461043)

© 2022 The GEN242 Instructors All Rights Reserved Privacy Policy