Mar 29-30, 2017
9:00 am - 4:30 pm
Instructors: Becca Love, Pariksheet Nanda
Helpers: Irem Celen, Modupe Adetunji, Mengxi Lv, Maddy Stinner
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.
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 firstname.lastname@example.org for more information.
Please be sure to complete these surveys before and after the workshop.
|Introduction, the data and the cloud|
|09:00||Intro to Data Carpentry||PN|
|09:15||Intro to the Data Set||PN|
|09:30||Connecting to the Cloud||PN|
|10:00||R and R Studio Orientation||PN|
|10:45||Dataframes and Metadata||PN|
|Aggregate, analyze and visualize with R|
|11:30||Data Cleaning and Manipulation with dplyr||BL|
|13:00||Data Cleaning and Manipulation with dplyr (cont'd)||BL|
|15:00||Plotting and visualization in R||BL|
|16:00||Intro to the Linux Shell - Filesystem and Navigation||PN|
|Shell, project setup, and sequence QC|
|09:00||Intro to the Linux Shell - Searching||BL|
|10:00||Quality Control of Sequencing Data||PN|
|11:30||Automating Analyses - Shell Scripting||BL|
|12:00||Lunch break and Tour of Sequencing Facility|
|Linux workflows to process genomics data|
|13:00||Automating Analyses - Shell Scripting||BL|
|14:00||Creating Workflows - Variant Calling Workflow||BL|
|14:45||Creating Workflows - Variant Calling Workflow (cont'd)||BL|
|15:30||Good programning practices||PN|
|16:00||Overview of Bioinformatics Facility||Staff|
|16:15||Wrap up and post-workshop survey||PN|
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
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.