CCDL RNA-Seq Workshop, Philadelphia, PA. Oct 14-16th, 2019
The Childhood Cancer Data Lab (CCDL) powered by Alex's Lemonade Stand Foundation is hosting a workshop to introduce childhood cancer researchers to reproducible analysis of bulk and single-cell transcriptomic data.
The workshop will last from 9AM to 5PM on October 14th, 15th, and 16th at the CCDL offices at 1429 Walnut St Philadelphia, PA, 19102.
This workshop is a fast-paced, hands-on introduction to RNA-seq analysis that aims to 1) prepare you to perform initial analyses of your own data, 2) increase your comfort level with reading documentation and learning how to apply new methods on your own and 3) give you the tools to collaborate more effectively with analysts when needed.
We have an example schedule of a course here with links to all the materials.
What we will teach you:
We cover selected pipelines for quality control, processing to gene expression estimates, and downstream analysis of bulk and single-cell RNA-seq data through hands-on exercises with brief discussions of the underlying methods.
Our workshop’s curriculum is generally designed to go broad and not deep.
What we won’t teach you:
We don’t address experimental design (e.g., how many replicates you need).
We won’t compare tools (e.g., edgeR vs. DESeq2 for differential gene expression).
We won’t cover every feature or assumption of the tools we do present, but we will try to highlight the features and gotchas that we think are relevant to most users.
You may not be able to perform every analysis you need to perform for your own work, particularly for complex experimental designs.
Participants will perform analyses on their own laptops. Participants must have a laptop running Windows 10 Professional or higher, Mac OS X, or a Linux operating system.
Some familiarity with the R programming language is strongly recommended. Participants that have no prior experience should plan to take an introductory self-taught course like Swirl. We will continue to practice these concepts in the context of gene expression data at the workshop.
We are able to provide hotel rooms, for which we cover the room rate and attendees cover the incidentals, for up to twenty out-of-town attendees for this workshop. Attendees are responsible for their own travel costs; however, those attending the Alex’s Lemonade Stand Foundation’s Young Investigator Summit may elect to book their travel such that it supports attending both events.
We will provide lunch each day and a workshop dinner one evening for all attendees.
Interested researchers must apply. The deadline to apply for the workshop is Sept 16th. Availability is limited. Researchers attending the Alex’s Lemonade Stand Foundation’s Young Investigator Summit who apply to the workshop before August 15, 2019 will receive priority. Next, preference will be given to researchers studying childhood cancers with biological questions related to transcriptomic data who apply before September 16th. Researchers studying cancer in general will be admitted if space is available. Applicants will be notified of their application status on a rolling basis.