CCDL RNA-Seq Workshop, Philadelphia, PA. Oct 14-16th, 2019
July 10, 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 will introduce you to the R programming language, R Notebooks, and some reproducible research practices.
- 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.
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 will introduce you to the R programming language, R Notebooks, and some reproducible research practices.
- 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.
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Hack4Rare is a virtual event that calls for healthcare startups, developers, solutions architects, and hackathon enthusiasts to join researchers, clinicians and patients in developing solutions built around a number of rare diseases including neurofibromatosis, PTEN Hamartoma Tumor Syndrome, RASopathies and Desmoid Tumors.
March 2, 2022
The workshop will take place on September 20 - 24, 2021 from noon - 5pm Eastern. Each day consists of lectures and designated time for attendees to work on exercise materials and their own projects with CCDL staff available for consultation.
March 2, 2022
Introducing refine.bio examples. Here, users can access a variety of example analyses implemented in R, such as clustering and heat maps, differential expression analysis, and pathway analysis, for use with refine.bio data.
March 2, 2022
The workshop will take place on November 1-5, 2021 from noon to 5pm eastern. Each day consists of lectures and designated time for attendees to work on exercise materials and their own projects with our staff available for consultation.
March 2, 2022
I work at the Childhood Cancer Data Lab, where we use very big data to find cures for childhood cancers. To move data around the internet at very high speeds, we are forced to use a proprietary software suite called Aspera. If somebody could make a Free Software alternative, the future of the internet would be way more awesome! Best of all, you can be the one to do it!
January 11, 2020
When my daughter Alex was diagnosed with cancer and throughout her battle, we saw how our community of people rallied around our family. No one knew quite how to help, but they were willing to do whatever was needed to ease the burden we faced.
January 11, 2020
'Work smarter not harder’ is useless advice if you don’t know how to ‘work smarter’. But the Childhood Cancer Data Lab's work and processes may be the smartest I’ve ever had the pleasure of learning and adopting.
March 2, 2022
The Data Lab will hold our first virtual workshop of the year from March 14-18, 2022!In this workshop, we will introduce researchers studying pediatric cancer to the R programming language, the Tidyverse R packages for data science, single-cell RNA-seq data analysis, and pathway analyses.
January 11, 2020
At the Data Lab, we are big proponents of automating the boring stuff so we can spend more time thinking about the fun stuff. But how exactly do we do that, and what does it mean to automate the boring stuff?
January 11, 2020
November marked the final Childhood Cancer Data Lab training workshop for 2021. We held four week-long virtual workshops this year, teaching 88 researchers the data science skills they need to examine their own data.
January 11, 2020
Before working as a Data Scientist at the Childhood Cancer Data Lab, I spent time in my PhD and post-doctoral fellowship in two very different research environments. Each had their own unique way of doing research. I found that some things worked really well and others were not as successful.
© Childhood Cancer Data Lab