Bioinformatics: Workshops and Working Groups

 


Bioinformatics Workshops

Please fill out this form if you are interested in a workshop.

 

We’re happy to announce new opportunities related to bioinformatic training and support for CAPS members and their research affiliates!  Workshops will be scheduled based on demand, so please use the above link to indicate your interest/availability.  Additional offerings will be announced in upcoming CAPS newsletters, as well as through social media.  We welcome suggestions for future areas of training that would benefit you and your lab groups.  In addition, we would love to hear from you if you might be open to offering some form of training in your area of expertise!

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New CAPS Bioinformatics Workshop:

Introduction to RMarkdown For Documenting and Sharing Your Code

 

Developing reproducible code and sharing results are two important parts of any bioinformatics task.  Rmarkdown provides a convenient framework for both writing and documenting code, and also executing the code to produce summary reports (e.g. pdf, html, etc).  This workshop provides an introduction to creating an Rmarkdown document, and then using that document to generate a report that includes the code itself, notes about the analysis, and results figures and tables generated by the code.  We also explore how code from programming languages outside of R (i.e. Perl, Python, Bash, etc) can be incorporated into these documents.  Basic knowledge of R and Command Line/Terminal are recommended for this workshop.

 

 

pitzerGetting Started: Utilizing High Performance Compute Resources

Analyses of large datasets, including bioinformatic datasets, often demand substantial computational resources.  In many cases, these are available as high-performance compute (HPC) clusters that are accessed remotely, either through a Terminal window, or a web browser.  In this workshop, participants will learn some of the basics of how to interact with a HPC resource, using the Ohio Supercomputer Center as an example.  After the workshop, participants will be able to describe the structure of the supercomputer environment, connect to and navigate on a supercomputer, submit basic batch jobs to the job scheduler, and monitor the status of the jobs.

 

 

Terminal WindowGetting Started: Working in Terminal

This one-hour workshop provides a basic introduction to command line computing within a Terminal window. Topics include navigating within Terminal, manipulating and organizing files and directories, downloading data files, and using basic wildcard characters (globbing).  Skills developed in this workshop are necessary for a wide range of bioinformatic tasks, including searching and manipulating large text-based data files and utilizing high-performance computing resources such as the Ohio Supercomputer Center or Amazon Web Services.

 

 

R Logo

Getting Started: Data Analysis with R

R is an open-source software environment for statistical computing that has become widely utilized within the field of bioinformatics, and more generally, data analytics.  This one-hour workshop provides a basic introduction to using R, and addresses specific topics such as installing and using R packages, understanding and using functions, importing data, and working with different types of R data structures.

 

 

RegexRegular Expressions for Searching and Editing Large Data Files

Regular expressions provide powerful methods for searching and editing text in large data files, and are implemented in a wide variety of informatic tools including R, various text editors, and at command line.  In this 1-2 hour workshop, we will work with regular expressions in both GUI-based text editors and command-line tools such as ‘grep’ and ‘sed’.  Participants will be introduced to some of the different types (flavors) of regular expressions, their associated syntax, and also some common pitfalls associated with their use.  A basic familiarity with working in Terminal (command line) is recommended, though not absolutely necessary for participating.

 

Getting Started with R

Getting Started: Data Visualization With R

One especially powerful aspect of R is its ability to produce high quality, customizable, publication-ready figures.  In this workshop, participants will be introduced to the fundamentals of two approaches for visualizing data in R – standard plotting functions that are available with the basic installation of R, and separately, ggplot, which is an R package for data visualization that provides even more flexibility and customization options.  

 

 

Data Viz

Data Visualization for ‘Omics Data in R

The scale of information produced in ‘omics studies can present challenges when it comes to creating figures that effective communicate results.  In this workshop, we’ll work with example ‘omics datasets to create some widely-used types of plots including volcano plots, heat maps, and Manhattan plots.  A basic understanding of R syntax is recommended for participating in this workshop

 

 

 


WORKING GROUP

Please fill out this form if you are interested in a working group.

 

RNAseq Working Groups

Need some assistance analyzing your own RNAseq dataset?   Don't yet have an RNAseq dataset, but would like to work through analyzing one?

Working groups will be assembled based on a combination of demand, analysis goals, and participants' availability. Mike Sovic will facilitate weekly meetings for each group, in which we will start with raw NGS reads and step through the analysis process. Basic command line and R skills are strongly recommended (see caps.osu.edu/bioinformatics for available workshops on these topics).

Working groups in Columbus will start as early as June, with groups in Wooster starting late summer/early fall.  Indicate your interest in joining an RNAseq working group by signing up here.  

 

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