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A Data Carpentry Workshop

University of Delaware

Mar 29-30, 2017

9:00 am - 4:30 pm

Instructors: Becca Love, Pariksheet Nanda

Helpers: Irem Celen, Modupe Adetunji, Mengxi Lv, Maddy Stinner

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.

We will cover Introduction, the data and the cloud, Aggregate, analyze and visualize with R, Shell, project setup, and sequence QC and Linux workflows to process genomics data. 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 aimed at graduate students and other researchers.

Where: Biotechnology Institute Room 102, 15 Innovation Way, Newark, DE 19711. 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 irem@udel.edu for more information.


Preliminary Schedule

Surveys

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

Pre-workshop Survey

Post-workshop Survey

Day 1

Introduction, the data and the cloud
09:00 Intro to Data Carpentry
09:15 Intro to the Data Set
09:30 Connecting to the Cloud
10:00 R and R Studio Orientation
10:30 Dataframes and Metadata
Aggregate, analyze and visualize with R
11:30 Data Cleaning and Manipulation with dplyr
12:00 Lunch break
13:00 Data Cleaning and Manipulation with dplyr (cont'd)
15:00 Plotting and visualization in R
16:00 Intro to the Linux Shell - Filesystem and Navigation

Day 2

Shell, project setup, and sequence QC
09:00 Intro to the Linux Shell - Searching and Metadata
10:00 Project Organization and Documentation
11:00 Quality Control of Sequencing Data
12:00 Lunch break
Linux workflows to process genomics data
13:00 Automating Analyses - Shell Scripting
14:00 Creating Workflows - Variant Calling Workflow
15:30 Data Importing and Uploading
16:30 Wrap up

Etherpad: http://pad.software-carpentry.org/2017-03-29-udel.
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.