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
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
Registration
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 ljsteele@stanford.edu for more information.
Workshop Surveys
Surveys
Please be sure to complete these surveys before and after the workshop.
Schedule
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 |
Etherpad: http://pad.software-carpentry.org/2017-01-22-stanford.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
Setup
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.