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Bioinformatics Workshop Videos

Introduction

INTRODUCTION

This series of R Workshops was offered in Spring 2018 by the USC Libraries Bioinformatics Service. The workshop series was designed specifically for beginners who have little or no prior knowledge of R, and teaches basic R usage with emphasis on typical bioinformatics tasks. This is a hands-on workshop where participants follow along with the instructor to learn and practice coding in R. The main objective of the workshop is to provide participants with a sufficient headstart to understanding the basic context and concepts of R, so as to enable subsequent self-learning of more advanced R topics. The video recordings of the workshops have now been edited for clarity and provided here.

WORKSHOP MATERIALS

Please download here the workshop materials (presentations, R scripts, example data, etc.).

PRE-REQUISITES

Participants are required to install two pieces of software (R and RStudio) on their own computers or laptops. The software installation instructions are provided with the workshop materials above. Usage of the instructional materials will be explained at the beginning of Lesson 1.

RECOMMENDED LEARNING METHOD

As with many other scripting- or coding-type languages, having hands-on practice, including (and especially) making mistakes serves well towards a better understanding and retention of the subject matter and the subtleties involved. There is no substitute for the experience gained working through the lecture material and testing out different scripting logic to getting a task performed (there are always multiple ways to get a job done). This is the investment that we advise you to commit to that will save you lots of frustrations down the road (trust us, we've been there!).  We therefore recommend that you work along with the video instructor on your own computer as if you are an on-site participant. If possible, play these videos on a second computer so you won't need to switch back and forth between windows. Good Luck!
 

INSTRUCTOR

Eddie Loh, PhD
Informatics Specialist (Bioinformatics)
USC Libraries Bioinformatics Services
Email: eddie.loh@usc.edu ; nmlbio@usc.edu
Web: https://libraries.usc.edu/person/eddie-loh

Lesson 1 Part 1

  Time       Chapters                                                                        
    0:00      1.01 - Workshop Introduction
    2:27      1.02 - Workshop Teaching Format
    4:57      1.03 - Introduction to R and RStudio
   10:42     1.04 - The R and RStudio Interface
   14:04     1.05 - Getting Situated in RStudio
   17:31     1.06 - Using Comment Lines, Set Working Directory
   26:22     1.07 - How To Use R Help Files
   38:30     1.08 - Objects, Variables, Classes
   47:14     1.09 - Data Structures: Vector
   58:08     1.10 - Data Structures: Factor, Matrix
1:07:43     1.11 - Data Structures: Data Frame, List
1:13:17     1.12 - Operators


Note: The workshop materials download link mentioned in the video is no longer valid, please refer to the link in the Introduction section above for the workshop materials packaged for these videos. 

Lesson 1 Part 2

  Time       Chapters                                                                        
    0:00      1.13 - A Small Example Dataset
    5:28      1.14 - Reading In and Displaying a Data File
   13:34     1.15 - Extracting a Subset of a Table (1/2)
   27:10     1.16 - Extracting a Subset of a Table (2/2)
   34:59     1.17 - Getting and Setting Data
   44:11     1.18 - Re-ordering a Table
   49:38     1.19 - Joining Text, Row and Column Binding
   54:25     1.20 - Merging Tables
1:04:52     1.21 - More Table Manipulations
1:13:35     1.22 - Writing Table to a File
1:20:25     1.23 - Misc Useful Commands, Practice Example
1:22:32     1.24 - Lesson 1 Summary

Lesson 2 Part 1

  Time       Chapters                                                                        
    0:00      2.01 - Reading in a Large Bioinformatics Data File
    5:27      2.02 - Using Grep to Search for Test
   20:48     2.03 - Substituting text with Sub
   31:52     2.04 - Application Scenario: Calculating Relative Position of Genes
   43:31     2.05 - Application Scenario: Further Manipulations, Using Apply
   51:50     2.06 - Installing R Packages from CRAN and BioConductor
1:01:50     2.07 - Plotting Graphs: Histograms and Barplots
1:10:31     2.08 - Plotting Graphs: Scatter and Bar Plots
1:24:34     2.09 - Plotting Graphs: More Tips and Tricks
1:32:25     2.10 - Workshop Closing Remarks
    Note:    Due to loss of some video footage and complexity of subject matter,

                 the section on EdgeR usage will not be posted. If you require help for

                 this analysis, please contact us at nmlbio@usc.edu.

Note: The workshop materials download link mentioned in the video is no longer valid, please refer to the link in the Introduction section above for the workshop materials packaged for these videos.