University of Connecticut

January 14-16, 2019

9:00 am - 5:00 pm

Instructors: Pariksheet Nanda, Kendra Maas, Asli Uyar, Cera Fisher, James Mickley, Timothy Moore

Helpers: Dyanna Louyakis, Dipanjana Dalui

Event Cancelled

This workshop is cancelled. Thank you for your interest! We hope to see you at a future Carpentries workshop.

General Information

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Innovation Partership Building (IPB) room 315, 159 Discovery Drive, Storrs, CT 06269. Get directions with OpenStreetMap or Google Maps.

When: January 14-16, 2019. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (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 Software Carpentry's Code of Conduct.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email pariksheet.nanda@uconn.edu for more information.


Surveys

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

Pre-workshop Survey

Post-workshop Survey


Schedule

Day 1: Monday, Jan 14

Before Pre-workshop survey
09:00 Workshop Overview
09:15 Introduction to R and RStudio
10:15 Project management with RStudio
10:30 Seeking help
10:45 Coffee
11:00 Data structures
12:00 Lunch break
13:00 Exploring Dataframes
13:30 Subsetting data
14:30 Coffee
14:45 Subsetting data (continued)
15:15 Control flow
16:00 Wrap-up

Day 2: Tuesday, Jan 15

09:00 Creating publication-quality graphics
10:45 Coffee
11:00 Vectorization
11:15 Functions explained
12:00 Lunch break
13:00 Writing data
13:30 Dataframe manipulation with dplyr
14:30 Coffee
14:45 Dataframe manipulation with tidyr
15:45 Producing reports with knitr
16:15 Wrap-up

Day 3: Wednesday, Jan 16

* Bioconductor is not yet formally part of the Carpentries curriculum
09:00 Workshop Overview
09:15 Introduction to Bioconductor
10:15 RNA-seq data analysis with DESeq2
10:30 Coffee
11:00 RNA-seq data analysis with DESeq2 (continued)
12:00 Lunch break
13:30 Solving common bioinformatic challenges using GenomicRanges
14:45 Coffee
15:00 Introduction to Bioconductor annotation
15:45 Public data resources and Bioconductor
16:45 Wrap-up
End Post-workshop Survey

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


Syllabus

Programming in R

  • Projects in RStudio
  • Working with vectors and data frames
  • Reading and plotting data
  • Creating and using functions
  • Loops and conditionals
  • Data frame manipulation
  • Producing reports
  • Reference...

Bioconductor for R Genomics

    * Bioconductor is not yet formally part of the Carpentries curriculum
  • Gene expression analysis
  • Working with genome coordinates
  • Reading annotations and public data

Setup

To participate in a Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

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.

R

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

Windows

Video Tutorial

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.

macOS

Video Tutorial

Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.

Linux

You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo dnf install R). Also, please install the RStudio IDE.