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A Data Carpentry Workshop

Stanford University School of Medicine

Jan 21-22, 2017

8:00 am - 5:00 pm

Instructors: Ryan Peek, Catalina Anghel

Helpers: Amy Hodge, Chris Beitel, Nikhil Damle, Chris Mark DeBoever, Joe Reese Davis III, Matt George Durrant, Lorraine Ling, Aparna Rajiv Rajpurkar, Genevieve L Wojcik, Zach Zappala


Please Register by January 10.

This workshop is brought to you by:



General Information

Data Carpentry workshops are for any researcher who has data they want to analyze, and no prior computational experience is required. This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data.

This is the Data Carpentry Genomics Workshop (overview page). The focus of this workshop is on working with genomics data and data management and analysis for genomics research. It covers metadata organization in spreadsheets, data organization, connecting to and using cloud computing, the command line for sequence quality control and bioinformatics workflows, and R for data analysis and visualization. The workshop does not teach any particular bioinformatics tools, but the foundational skills that will allow you to conduct any analysis and analyze the output of a genomics pipeline. Participants should bring their laptops and plan to participate actively. By the end of the workshop learners should be able to more effectively manage and analyze data and be able to apply the tools and approaches directly to their ongoing research.

Who: The course is for Stanford graduate students only. This offering of Data Carpentry can be taken for academic credit

Where: Li Ka Shing Center for Learning and Knowledge Room LK120, 291 Campus Drive, Stanford, California, 94305. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating sytem (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Data Carpentry's Code of Conduct.

Contact: Please mail for more information.

Workshop Surveys


Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey


Day 1: 8:30AM - 5:00PM

8:00 - 8:30: Coffee & Sign In
Morning: Intro, The Data, and The Cloud
Intro to Data Carpentry Ryan
Intro to Data Catalina
Genomics Data Tidyness Catalina
Connecting to the Cloud in 5 Minutes or Less Ryan
RStudio Orientation, Intro to R Ryan
Dataframes and Metadata Ryan
Afternoon: Shell, Project Setup, and Sequence QC
Using the Command Line (Shell) Catalina
Data Importing and Uploading Ryan
Project Setup & Organization Catalina
QC of Sequence Data Catalina

Day 2: 8:30AM - 5:00PM

8:00 - 8:30: Coffee & Sign In
Morning: Using Linux Workflows to Process Genomics Data
Automating Workflows Catalina
Variant Calling Catalina
Genomics and R Ryan
Dataframes and R Ryan
Afternoon: Aggregate, Analyze, Visualize with R
Aggregate and Analyze with dplyr Ryan
Visualization with ggplot2 Ryan
Workshop Conclusion Please take the Post-workshop Survey

Post Workshop

How to Make This Work on Your Own
Launching Your Own Cloud Instances On Your Own

We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.


To participate in a Data Carpentry workshop, you will need working copies of the described software. Please make sure to install everything (or at least to download the installers) before the start of your workshop. Participants should bring and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop.

Please follow these Setup Instructions.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.