Syllabus and reference files for Software Carpentry

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Here you will find data files, reference sheets, and teaching notes for the workshop. We may not cover all of this material or do so in the order provided, but you will have the material as a reference after the workshop.

Remember that additional notes, links, etc. will be found on the Etherpad.

R (Day 1)

Download the data for the R lessons here: gapminder-FiveYearData.csv

1. Introduction to R and RStudio
2. Project Management
3. Seeking help
4. Data types and structures
5. Data structures: data frames
6. Subsetting data

R Reference Sheet

The UNIX Shell

• Download the data for the shell lesson here: shell-genomics.zip

1. Introducing the shell for automation
   Slides

Shell Reference Sheet

Version Control with Git

1. Introducing version control
2. A better kind of backup
3. Collaborating
4. Conflicts
5. Open science

Git Reference Sheet

R (day 2)

Download the (same) data for the R lessons here: gapminder-FiveYearData.csv

1. Plotting
2. R Markdown
3. Capstone exercise

R Reference Sheet

Other R Topics

1 Writing Functions 2. Vectorisation 3. Control flow