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A Data Carpentry Workshop

University of Cambridge

Sep 10-11, 2015

9:30 - 17:30

Instructors: Laurent Gatto, Krzysztof Strug

Helpers: Gabriella Rustici

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 Data organization in spreadsheets and OpenRefine, Introduction to R, Data analysis and visualization in R and SQL for data management. 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: Bioinformatics Training Room, Craik-Marshall Building, Downing Site. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below). They are also required to abide by Data Carpentry's Code of Conduct.

Contact: Please mail Gabriella Rustici for more information.

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



Day 1

Data organization in spreadsheets

  1. Introduction
  2. Formatting data
  3. Common formatting problems
  4. Dates as data
  5. Quality control
  6. Exporting data
  7. Data Format Caveats (optional)

Data files for the lesson are available here.

Data cleaning with OpenRefine

  1. Getting Started with OpenRefine
  2. Working with OpenRefine - faceting, clustering & splitting
  3. Scripts
  4. Saving and Exporting Projects and Files

Data files for the lesson are available here here.

Introduction to R

  1. Before we start
  2. Introduction to R
  3. Starting with data
  4. Introducing data.frame

Day 2

Data analysis and visualization in R

  1. Data analysis
  2. Data visualisation with ggplot2

SQL for data management

  1. Introduction to SQL
  2. Basic queries
  3. Aggregation
  4. Joins and aliases
  5. R and SQL (optional)
  6. SQL solutions

Data files for the workshop are available here.


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.