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Projects

March 2, 2022

Introducing the ScPCA downstream analysis workflow!

At the Data Lab, we are constantly looking for ways to enhance the tools we build for pediatric cancer researchers. Earlier this year, we launched the Single-cell Pediatric Cancer Atlas portal, a database of uniformly-processed single-cell data from pediatric cancer clinical samples. One way we felt the portal could be even more beneficial to pediatric cancer researchers is with a ready-to-go workflow that takes in single-cell data and prepares it for downstream analyses such as unsupervised clustering. 

Projects

March 2, 2022

Teaching with live coding in R and RStudio

The Data Lab teaches data science courses targeted toward pediatric cancer researchers that introduce topics such as analysis of gene expression in bulk and single-cell data and principles of reproducible research. I wrote previously about how we use RStudio Server for our remote courses to simplify setup, and I wanted to write a bit more about some of the instructional practices we use so that our participants get the best experience we can provide. In particular, I wanted to talk about our use of live coding to facilitate active learning, and one of the tools we developed to make our course development just a bit easier.

Projects

March 2, 2022

Introducing the Single-cell Pediatric Cancer Atlas (ScPCA) Portal

The Single-cell Pediatric Cancer Atlas (ScPCA) Portal project began in 2019 when Alex’s Lemonade Stand Foundation (ALSF) funded 10 awards for single-cell profiling of pediatric cancer samples. The goal was to produce an atlas of gene expression profiles for a variety of childhood cancer types from different organ sites.

Projects

March 2, 2022

How does big data help us tackle childhood cancer?

MultiPLIER is a machine learning approach that brings big data to bear on rare diseases. It’s also an example of the scientific approach and ethos of the CCDL, and the publication is a great opportunity to share how the CCDL is developing new technologies to accelerate research into cures for childhood cancers!

Projects

March 2, 2022

Does Bulk Tissue Still Belong in a Single-Cell Atlas?

Earlier this year, Alex’s Lemonade Stand Foundation identified single-cell gene expression profiling as an opportunity to build an atlas of cell types within tumors that could be broadly reused by pediatric cancer researchers.

Projects

March 2, 2022

Exploring neurofibromatosis data with refine.bio

I’m a scientist at Sage Bionetworks, a nonprofit research organization in Seattle, WA. My work focuses on a family of rare pediatric diseases (NF): neurofibromatosis type 1, type 2, and schwannomatosis.

Projects

March 2, 2022

3 things the CCDL is doing right now to keep pediatric cancer research moving forward

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.

Projects

March 2, 2022

OpenPBTA: Someone is wrong on the internet and it’s probably us (updated 9-9-2020)

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).

Projects

March 2, 2022

Introducing Example Analyses for Use with refine.bio Data

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.

Projects

March 2, 2022

A Desperate Plea for a Free Software Alternative to Aspera

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!