Full: CCDL Single-Cell RNA-Seq Workshop, Virtual, November 1st-5th, 2021
September 28, 2021
The Data Lab will hold our next virtual workshop running from November 1-5, 2021!
In this workshop, Data Lab staff 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.
Virtual Workshop Structure
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. On Friday, November 5th, we will cover any final questions and allow you to present the projects you have worked on to the other workshop participants. View a past workshop schedule here to see what you can expect!
During lectures, Data Lab staff will lead you through course material using Zoom, Slack, and RStudio Server. We will record instruction and provide it to workshop attendees so they can revisit it outside of workshop hours or in case they experience disruptions during live instruction.
During consultation time, our staff will be available to answer questions and provide any 1:1 assistance as you work through exercise notebooks we provide or work with your own transcriptomic data. We’ll use Zoom and Slack for this, too.
You’ll need a laptop with internet access and to install Zoom & Slack. You will log into an RStudio Server hosted by the Data Lab from your web browser.
What you will learn
- We will introduce you to the R programming language, R Notebooks, and some reproducible research practices.
- We will introduce selected pipelines for single-cell RNA-seq analysis through hands-on exercises and brief discussions of the underlying methods. Topics covered will include quality control, normalization, clustering, and visualization.
- We will introduce common approaches for pathway analysis.
- Our workshop’s curriculum is generally designed to go broad and not deep.
We do not assume prior programming experience, but the course will move quickly and we have assembled some resources for learning R basics to help make the most of our time together.
What you won’t learn
- We don’t address experimental design (e.g., how many replicates you need).
- We won’t compare tools (e.g., Seurat vs. Scater for single-cell RNA-seq data pre-processing).
- 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 for your own work, particularly for complex experimental designs.
Apply Now!
If you are a pediatric cancer researcher and this sounds like it’s for you, please apply now!
To ensure that workshop attendees have a great hands-on experience, there will be a very limited number of seats available. We will prioritize applicants that have single-cell transcriptomic data that they are currently using to answer questions in pediatric cancer research. Please feel free to reach out to us at training@ccdatalab.org with any questions.
For full consideration, please apply by Monday, October 11th. Applicants will be notified of their acceptance after registration is closed and all applications have been reviewed. Accepted workshop participants will be asked to provide a $100 deposit to reserve their seat. Deposits will be fully refunded upon workshop attendance.
The Data Lab will hold our next virtual workshop running from November 1-5, 2021!
In this workshop, Data Lab staff 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.
Virtual Workshop Structure
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. On Friday, November 5th, we will cover any final questions and allow you to present the projects you have worked on to the other workshop participants. View a past workshop schedule here to see what you can expect!
During lectures, Data Lab staff will lead you through course material using Zoom, Slack, and RStudio Server. We will record instruction and provide it to workshop attendees so they can revisit it outside of workshop hours or in case they experience disruptions during live instruction.
During consultation time, our staff will be available to answer questions and provide any 1:1 assistance as you work through exercise notebooks we provide or work with your own transcriptomic data. We’ll use Zoom and Slack for this, too.
You’ll need a laptop with internet access and to install Zoom & Slack. You will log into an RStudio Server hosted by the Data Lab from your web browser.
What you will learn
- We will introduce you to the R programming language, R Notebooks, and some reproducible research practices.
- We will introduce selected pipelines for single-cell RNA-seq analysis through hands-on exercises and brief discussions of the underlying methods. Topics covered will include quality control, normalization, clustering, and visualization.
- We will introduce common approaches for pathway analysis.
- Our workshop’s curriculum is generally designed to go broad and not deep.
We do not assume prior programming experience, but the course will move quickly and we have assembled some resources for learning R basics to help make the most of our time together.
What you won’t learn
- We don’t address experimental design (e.g., how many replicates you need).
- We won’t compare tools (e.g., Seurat vs. Scater for single-cell RNA-seq data pre-processing).
- 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 for your own work, particularly for complex experimental designs.
Apply Now!
If you are a pediatric cancer researcher and this sounds like it’s for you, please apply now!
To ensure that workshop attendees have a great hands-on experience, there will be a very limited number of seats available. We will prioritize applicants that have single-cell transcriptomic data that they are currently using to answer questions in pediatric cancer research. Please feel free to reach out to us at training@ccdatalab.org with any questions.
For full consideration, please apply by Monday, October 11th. Applicants will be notified of their acceptance after registration is closed and all applications have been reviewed. Accepted workshop participants will be asked to provide a $100 deposit to reserve their seat. Deposits will be fully refunded upon workshop attendance.
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To help keep pediatric cancer research moving forward, here are 3 ways the CCDL is helping the research community during this time: refine.bio, virtual workshops, and the Open Pediatric Brain Tumor Atlas project.
March 2, 2022
We know that pandemic-related university closures mean that the demand for opportunities for pediatric cancer researchers to increase their analytical skills has never been higher. As such, we are delighted to announce a pilot virtual workshop running from May 4-8, 2020!
March 2, 2022
Here at the Childhood Cancer Data Lab, we value transparency and the practice of open science. Much of the work we’ve done and the products that we build hinge on the generosity and openness of other scientists. In this post, as part of National Brain Tumor Awareness month, we want to talk about a project that our science team has been working on over the last few months (and to do so in a way that aligns with our values).
March 2, 2022
The workshop will take place on June 22 - 26, 2020 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.
January 11, 2020
When the CCDL (along with everyone else) realized that we would have to conduct our bioinformatics training workshops remotely, we had to make some quick decisions about how we were going to do it. Most of the instructional materials for our in person workshops were already online, so we knew we had a good base to work from. We just needed to figure how to adapt the live instruction.
March 2, 2022
At Alex’s Lemonade Stand Foundation’s Childhood Cancer Data Lab, we’re excited to be helping out with an upcoming event hosted by the Children’s Tumor Foundation. If you participate, you may meet members of our team who are mentoring and judging.
March 2, 2022
The workshop will take place on March 22 - 26, 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
The workshop will take place on June 28- July 2, 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 CCDL staff available for consultation.
March 2, 2022
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
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.
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