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.
We put together the ScPCA downstream analysis workflow to filter, normalize, and perform dimensionality reduction, as well as incorporate initial clustering results to each processed sample/library object.
What the workflow does
The workflow takes in pre-processed gene expression data stored as a SingleCellExperiment object (filtered to remove empty cells/droplets), and performs the following steps:
- Filtering - Each library is filtered to remove any low quality cells using either miQC::filterCells() or through setting a series of manual thresholds (e.g. the minimum number of UMI counts). Genes found in a low percentage of cells in each library are also removed at this step.
- Normalization - Cells are normalized using the deconvolution method from Lun, Bach, and Marioni (2016). The normalized log counts are stored in the SingleCellExperiment object returned by the workflow.
- Dimensionality Reduction - Reduced dimensions are calculated using both principal component analysis (PCA) and uniform manifold approximation and projection (UMAP). The embeddings from PCA and UMAP can be found in the SingleCellExperiment object returned by the workflow.
- Clustering - Cells are assigned to cell clusters using graph-based clustering. By default, louvain clustering is performed using the bluster::NNGraphParam() function with a default nearest-neighbors parameter of 10. Alternatively, walktrap graph-based clustering can be specified, and the number of nearest neighbors parameter can be altered if desired. Cluster assignments are stored in the SingleCellExperiment object returned by the workflow.
What the workflow does not do
The workflow is meant to be a user-friendly, ready-to-go workflow that will perform the core steps often needed when analyzing single-cell data. However, there are a few things that the workflow will not do:
- The workflow will not pre-process your data. Instead, you can see our scpca-nf workflow and ScPCA Portal docs for our suggested approach to pre-processing your data before implementing this workflow, which includes filtering to remove empty cells/droplets.
- The workflow will not convert your data into a SingleCellExperiment object, which means that if your data exists in other formats (e.g. a Seurat object), you will need to perform the initial conversion yourself.
- The workflow will not make decisions about your data. You will be provided with results based on the parameters used throughout the workflow, but we do not do the science for you! You will need to look at the results for yourself to interpret whether or not they are reasonable. Decision making can be highly dependent on the needs of individual researchers, so making such decisions for everyone would not be possible or beneficial.
Workflow requirements
To run the downstream analyses workflow on your own sample data, you will need the following:
- Single-cell gene expression data stored as SingleCellExperiment objects in RDS files. The workflow is set up to process data available on the Single-cell Pediatric Cancer Atlas portal and output from the scpca-nf workflow where single-cell/single-nuclei gene expression data is mapped and quantified using alevin-fry. For more information on this pre-processing, please see the ScPCA Portal docs. Note however that the input for this pipeline is not required to be scpca-nf processed output; the only requirement is that gene expression data be stored as a SingleCellExperiment object in an RDS file.
- A project metadata tab-separated value (TSV) file containing relevant information about the sample data necessary for processing, as described in the metadata file format section of the GitHub repository’s README file.
- A mitochondrial gene list that is specific to the genome or transcriptome version used for alignment. The workflow will use the mitochondrial gene list obtained from Ensembl version 104 by default. This gene list can be found in the reference-files directory of the Github repository.
- A local installation of Snakemake and either R or conda. (See more on this in the how to install the core downstream analyses workflow section.)
Expected output
For each SingleCellExperiment associated with an individual library, the workflow will return two files: a processed SingleCellExperiment object stored in an RDS file containing normalized data and clustering results, and a summary HTML report detailing the filtering of low-quality cells, dimensionality reduction, and clustering that was performed within the workflow. Below is an example of the expected output file structure.
The first output file is the *<library_id>_<filtering_method>_processed_sce.rds file, where `library_id` is the unique library and `filtering_method` is one of miQC or manual. This is the RDS file that contains the final processed SingleCellExperiment object, which contains the filtered, normalized data and clustering results. Clustering results can be found in the colData of the SingleCellExperiment object, stored in a metadata column named using the associated clustering type and nearest neighbors values.
The *<library_id>_<filtering_method>_core_analysis_report.html file is the html file that contains the summary report of the filtering, dimensionality reduction, and clustering results associated with the processed SingleCellExperiment object.
Walk through an example with us!
After ensuring that all of the required software is installed on your machine, as described in the how to install the core downstream analyses workflow section of the GitHub repository’s README file, we are ready to get started with the workflow!
Step 1 - Set up input data
Once you confirm that your single-cell gene expression data has been stored as SingleCellExperiment objects within RDS files, where each RDS file is associated with a single library id, you are ready to set up the project metadata file.
Create a new TSV file, where each row corresponds to a unique library and the columns contain the information associated with that library, and save it in the project-metadata directory. Below is an example of the columns and values that should be in the project metadata TSV file. See more on the columns and their expected values at the metadata file format section of the Github repository’s README.
Step 2 - Run the workflow via command line
Now we can run the snakemake workflow via the command line. To run the workflow we will also need to specify a few parameters, such as where to store the output, the path to the project metadata file, and the path to the mitochondrial gene list. We specify this information using the--config flag which allows us to override their default values for the relevant variables found in the config.yaml file. Below is an example of running the workflow via the command line while modifying only the necessary config file variables.
Step 3 - Check output!
Upon successful completion of the workflow, you should have two output files per sample/library id specified in the project metadata file. Below is the output of the test sample data we ran.
How to get started!
If you are interested in trying the ScPCA downstream analysis workflow on your data or are just curious to learn a bit more about how it works, you can get started with the README associated with the GitHub repository! We also have provided documentation with further details on the processing steps and decisions made throughout the workflow.
Additionally, if you are interested in participating in usability testing of the downstream analysis workflow, please fill out this form and we will contact you when we are ready for testing!
If you have questions about the ScPCA portal, you can reach out to us at scpca@ccdatalab.org!
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.
We put together the ScPCA downstream analysis workflow to filter, normalize, and perform dimensionality reduction, as well as incorporate initial clustering results to each processed sample/library object.
What the workflow does
The workflow takes in pre-processed gene expression data stored as a SingleCellExperiment object (filtered to remove empty cells/droplets), and performs the following steps:
- Filtering - Each library is filtered to remove any low quality cells using either miQC::filterCells() or through setting a series of manual thresholds (e.g. the minimum number of UMI counts). Genes found in a low percentage of cells in each library are also removed at this step.
- Normalization - Cells are normalized using the deconvolution method from Lun, Bach, and Marioni (2016). The normalized log counts are stored in the SingleCellExperiment object returned by the workflow.
- Dimensionality Reduction - Reduced dimensions are calculated using both principal component analysis (PCA) and uniform manifold approximation and projection (UMAP). The embeddings from PCA and UMAP can be found in the SingleCellExperiment object returned by the workflow.
- Clustering - Cells are assigned to cell clusters using graph-based clustering. By default, louvain clustering is performed using the bluster::NNGraphParam() function with a default nearest-neighbors parameter of 10. Alternatively, walktrap graph-based clustering can be specified, and the number of nearest neighbors parameter can be altered if desired. Cluster assignments are stored in the SingleCellExperiment object returned by the workflow.
What the workflow does not do
The workflow is meant to be a user-friendly, ready-to-go workflow that will perform the core steps often needed when analyzing single-cell data. However, there are a few things that the workflow will not do:
- The workflow will not pre-process your data. Instead, you can see our scpca-nf workflow and ScPCA Portal docs for our suggested approach to pre-processing your data before implementing this workflow, which includes filtering to remove empty cells/droplets.
- The workflow will not convert your data into a SingleCellExperiment object, which means that if your data exists in other formats (e.g. a Seurat object), you will need to perform the initial conversion yourself.
- The workflow will not make decisions about your data. You will be provided with results based on the parameters used throughout the workflow, but we do not do the science for you! You will need to look at the results for yourself to interpret whether or not they are reasonable. Decision making can be highly dependent on the needs of individual researchers, so making such decisions for everyone would not be possible or beneficial.
Workflow requirements
To run the downstream analyses workflow on your own sample data, you will need the following:
- Single-cell gene expression data stored as SingleCellExperiment objects in RDS files. The workflow is set up to process data available on the Single-cell Pediatric Cancer Atlas portal and output from the scpca-nf workflow where single-cell/single-nuclei gene expression data is mapped and quantified using alevin-fry. For more information on this pre-processing, please see the ScPCA Portal docs. Note however that the input for this pipeline is not required to be scpca-nf processed output; the only requirement is that gene expression data be stored as a SingleCellExperiment object in an RDS file.
- A project metadata tab-separated value (TSV) file containing relevant information about the sample data necessary for processing, as described in the metadata file format section of the GitHub repository’s README file.
- A mitochondrial gene list that is specific to the genome or transcriptome version used for alignment. The workflow will use the mitochondrial gene list obtained from Ensembl version 104 by default. This gene list can be found in the reference-files directory of the Github repository.
- A local installation of Snakemake and either R or conda. (See more on this in the how to install the core downstream analyses workflow section.)
Expected output
For each SingleCellExperiment associated with an individual library, the workflow will return two files: a processed SingleCellExperiment object stored in an RDS file containing normalized data and clustering results, and a summary HTML report detailing the filtering of low-quality cells, dimensionality reduction, and clustering that was performed within the workflow. Below is an example of the expected output file structure.
The first output file is the *<library_id>_<filtering_method>_processed_sce.rds file, where `library_id` is the unique library and `filtering_method` is one of miQC or manual. This is the RDS file that contains the final processed SingleCellExperiment object, which contains the filtered, normalized data and clustering results. Clustering results can be found in the colData of the SingleCellExperiment object, stored in a metadata column named using the associated clustering type and nearest neighbors values.
The *<library_id>_<filtering_method>_core_analysis_report.html file is the html file that contains the summary report of the filtering, dimensionality reduction, and clustering results associated with the processed SingleCellExperiment object.
Walk through an example with us!
After ensuring that all of the required software is installed on your machine, as described in the how to install the core downstream analyses workflow section of the GitHub repository’s README file, we are ready to get started with the workflow!
Step 1 - Set up input data
Once you confirm that your single-cell gene expression data has been stored as SingleCellExperiment objects within RDS files, where each RDS file is associated with a single library id, you are ready to set up the project metadata file.
Create a new TSV file, where each row corresponds to a unique library and the columns contain the information associated with that library, and save it in the project-metadata directory. Below is an example of the columns and values that should be in the project metadata TSV file. See more on the columns and their expected values at the metadata file format section of the Github repository’s README.
Step 2 - Run the workflow via command line
Now we can run the snakemake workflow via the command line. To run the workflow we will also need to specify a few parameters, such as where to store the output, the path to the project metadata file, and the path to the mitochondrial gene list. We specify this information using the--config flag which allows us to override their default values for the relevant variables found in the config.yaml file. Below is an example of running the workflow via the command line while modifying only the necessary config file variables.
Step 3 - Check output!
Upon successful completion of the workflow, you should have two output files per sample/library id specified in the project metadata file. Below is the output of the test sample data we ran.
How to get started!
If you are interested in trying the ScPCA downstream analysis workflow on your data or are just curious to learn a bit more about how it works, you can get started with the README associated with the GitHub repository! We also have provided documentation with further details on the processing steps and decisions made throughout the workflow.
Additionally, if you are interested in participating in usability testing of the downstream analysis workflow, please fill out this form and we will contact you when we are ready for testing!
If you have questions about the ScPCA portal, you can reach out to us at scpca@ccdatalab.org!
Related Post
In our last blog post, we shared some of the tools and methods we are using in the Open Single-cell Pediatric Cancer Atlas (OpenScPCA) project to ensure that the analysis code remains usable and runnable throughout the project. That post mainly focused on some of the most dynamic phases of the project, when contributors are adding new analysis modules and updating existing ones with more refined results. Here, we will discuss the test data that enables the methods and our approach to running the full set of analyses on real data.
Applications are open for the Data Lab's next training workshop! We will cover advanced topics in the analysis of single-cell RNA-seq data for researchers studying pediatric cancer. The 3-day course will take place December 10-12, 2024 from 9am-5pm Eastern time in Bala Cynwyd, PA, just outside of Philadelphia.
Earlier this year, we launched the Open Single-cell Pediatric Cancer Atlas (OpenScPCA) project, a collaborative project to openly analyze the data in the Single-cell Pediatric Cancer Atlas Portal on GitHub. We hope this project will bring transparently and expertly assigned cell type labels to the data in the Portal, help the community understand the strengths and limitations of applying existing single-cell methods to pediatric cancer data, and, frankly, allow us to meet more scientists in our community working with single-cell data (maybe you? 😄).
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So you recently did some single-cell RNA sequencing and are working on analyzing your data. You’ve already quantified the gene expression data, performed any filtering, and normalized your data, but now what? You know you want to perform differential expression analysis or that you need to annotate the cell types found in your data, but there are so many different tools and methods for performing these analyses. How do you know which one is the best method for your dataset? Don’t worry, we’ve all been there – even experts in the single-cell field have been there.
The Open Single-cell Pediatric Cancer Atlas (OpenScPCA) is an open, collaborative project to analyze data from the Single-cell Pediatric Cancer Atlas (ScPCA) Portal, which currently holds over 500 samples from over 50 pediatric cancer types. OpenScPCA uses an open contribution model designed to allow experts worldwide to contribute and rapidly share the results of analyses in real time. The project was officially launched in April 2024.
In March 2022, we launched the Single-cell Pediatric Cancer Atlas (ScPCA) Portal to make uniformly processed single-cell and single-nuclei RNA-Seq data widely available to the childhood cancer research community. Initially, all data available on the Portal was generated through grants funded by Alex’s Lemonade Stand Foundation (ALSF) as part of the ScPCA project. But enabling access to ALSF-funded data was just the beginning of our vision.Sharing is key to ensuring the Portal’s continued growth. Our sights were set on allowing more pediatric cancer researchers to contribute data to the ScPCA Portal.
The Data Lab has just launched the brand new Open Single-cell Pediatric Cancer Atlas (OpenScPCA) project! This open, collaborative project aims to analyze data from the ScPCA Portal, which currently holds 500 samples from over 50 pediatric cancer types. We are seeking contributors with diverse skills and expertise to join the project!
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Are you attending the American Association for Cancer Research (AACR) annual meeting in San Diego, CA? Visit the Alex’s Lemonade Stand Foundation (ALSF) Grants and Data Lab teams at booth 3755 in the exhibit hall from April 7-10 and during poster sessions on April 8. We will announce a new collaborative project and share exciting news about the Single-cell Pediatric Cancer Atlas Portal and training opportunities!
Did you know that 70% of the Alex’s Lemonade Stand Foundation (ALSF) Childhood Cancer Data Lab team are currently women? Advancing our mission to empower childhood cancer researchers with knowledge, data, and tools would not be possible without their expertise. On the International Day of Women and Girls in Science, we are excited to introduce you to these women who integrate science, engineering, and design to tackle some of the greatest challenges faced by the pediatric cancer research community!
I have a confession to make: I am lazy. Ok, maybe that's too strong. Let's go for a euphemism instead: I am efficient. I love learning handy tricks that make my life easier and make my job smoother with fewer hiccups along the way. This is one part of why, here in the Data Lab, we love automation - why waste our time on rote, repetitive, housekeeping tasks when we can get the bots to do it for us? In this blog post, we'll highlight a few tips about how you can use RStudio to code more efficiently.
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In 2019, Alex’s Lemonade Stand Foundation (ALSF) established the Single-cell Pediatric Cancer Atlas (ScPCA) through awards for data generation and to create an atlas of single-cell gene expression profiles of pediatric cancers of different types and from different organ sites. The Data Lab launched the ScPCA Portal in 2022 to make uniformly processed, summarized single-cell and single-nuclei RNA-seq data and de-identified metadata available for download. The ScPCA Portal also supports other data modalities, such as bulk RNA-seq, CITE-seq, and spatial transcriptomics. The ScPCA Portal currently hosts data for over 500 pediatric tumor and patient-derived xenograft samples from more than 50 cancer types, and continues to grow. The Data Lab is seeking contributions to the ScPCA Portal from researchers with existing single-cell datasets.
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Are you attending the American Association for Cancer Research (AACR) annual meeting in Orlando, FL this year? Visit Alex's Lemonade Stand Foundation (ALSF) at booth 369 in the exhibit hall from April 16-19! You'll find information about ALSF's grants program, the Childhood Cancer Data Lab and more. The Data Lab will also be holding office hours during select time slots.
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Welcome to the Data Lab’s December Scientific Community Bulletin! Each month we share upcoming opportunities from Alex’s Lemonade Stand Foundation (ALSF), the Data Lab, and other events that we have gathered from a variety of science and research organizations. Subscribe to our blog to be alerted about future Scientific Community Bulletin posts!
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Welcome to the Data Lab’s November Scientific Community Bulletin! Each month we share upcoming opportunities from Alex’s Lemonade Stand Foundation (ALSF), the Data Lab, and other events that we have gathered from a variety of science and research organizations. Subscribe to our blog to be alerted about future Scientific Community Bulletin posts!
Here at the Data Lab, we're all about, well, data! We believe that data sharing and accessibility is key to accelerating the research process, and ultimately to improving outcomes for childhood cancer patients. So, we were excited to learn that one of the goals of the NCI/NIH initiative, the Childhood Cancer Data Initiative (CCDI), is to build up a Data Ecosystem that will facilitate pediatric cancer researchers' ability to explore and collect data from disparate resources. Although this Ecosystem is still in the early stages, several components are already being developed and are available for researchers to use! One component that is particularly interesting to us is the CCDI's Childhood Cancer Data Catalog (CCDC).
Welcome to the October Scientific Community Bulletin! Each month we share upcoming opportunities from Alex’s Lemonade Stand Foundation (ALSF), the Data Lab, and other events that we have gathered from a variety of science and research organizations. Subscribe to our blog to be alerted about future Scientific Community Bulletin posts!
Welcome to the September Scientific Community Bulletin! Each month we share upcoming opportunities from Alex’s Lemonade Stand Foundation (ALSF), the Data Lab, and other events that we have gathered from a variety of science and research organizations. Subscribe to our blog to be alerted about future Scientific Community Bulletin posts!
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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.
Welcome to the August Scientific Community Bulletin! Each month we share upcoming opportunities from Alex’s Lemonade Stand Foundation (ALSF), the Data Lab, and other events that we have gathered from a variety of science and research organizations.
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Welcome to the July Scientific Community Bulletin! Each month we share upcoming opportunities from Alex’s Lemonade Stand Foundation (ALSF), the Data Lab, and other events that we have gathered from a variety of science and research organizations. Subscribe to our blog to be alerted about future Scientific Community Bulletin posts!
Welcome to the Childhood Cancer Data Lab’s new blog feature, the monthly Scientific Community Bulletin! At the start of each month, we will share upcoming opportunities from Alex’s Lemonade Stand Foundation (ALSF), the Data Lab, and other events that we have gathered from a variety of science and research organizations. Our goal is to promote learning opportunities and highlight some of the excellent resources that our community provides.
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The Childhood Cancer Data Lab builds resources guided by the most pressing needs of our primary users: pediatric cancer researchers. As the Data Lab's UX Designer, I conduct research activities with scientists like usability evaluations, semi-structured interviews, and card sorts to gain insight into their activities, processes, pain-points, and behaviors. I work with scientists and engineers at the Data Lab to use this information to improve existing products and services or to create new ones.
The Data Lab is excited to announce that our next training workshop is taking place in-person on Friday, June 10, 2022! During this full day workshop, instructors will introduce principles and techniques to achieve reproducible results in computational cancer research. We’ll show you the fundamentals of commonly-used approaches in reproducibility that you can apply to increase the impact of your research by making your findings more robust and reliable!
The Childhood Cancer Data Lab is growing as a resource for pediatric cancer researchers and we have more to offer to our community now, than ever before. Transitioning to our new and improved website is an exciting milestone, and here, we look forward to sharing progress, introducing new initiatives, and cultivating more opportunities to support childhood cancer research. Welcome to our new virtual home!
The Single-cell Pediatric Cancer Atlas (ScPCA) 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.
The CCDL team includes science, engineering, and design expertise. Combining these three disciplines in different ways across projects enables us to carry out our mission.
Here at the CCDL we value putting publicly available data to work. For example, we are currently processing and normalizing 1.5 million publicly available gene expression samples totaling ~$1.5 billion research dollars expended.
Like many teams that work with large amounts of external software, we run into issues with our transitive dependencies. In general, transitive dependencies are a hard problem to solve.
Though technology can introduce great benefit into our lives, it is often accompanied by a substantial amount of time and some expected frustration before we can reap the rewards. The time spent learning a new technology is what we usually call a learning curve.
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.
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!
The Childhood Cancer Data Lab 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 Childhood Cancer Data Lab (CCDL), an initiative of Alex's Lemonade Stand Foundation develops tools, trainings, and methods to empower childhood cancer researchers. The work at the CCDL is focused and impactful. There are multiple opportunities and challenges for you to apply and grow your skills as a scientist or as an engineer.
The Childhood Cancer Data Lab 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.
At this hands-on, 3-day session held in Houston, researchers learned data science skills that could accelerate their own work. Drawing on skills learned at the workshop, childhood cancer researchers can perform basic analyses of their work to make informed decisions on how to proceed with their own research. Don’t just take our word for it, though. Read more about the workshop’s incredibly valuable benefits through its attendees’ perspectives.
The goal of our refine.bio project is to download, process, and make available gene expression datasets that can be analyzed together, or in parts, depending on a researcher’s need. Childhood cancer researchers need to be able to use data generated through multiple profiling technologies including microarrays and RNA-sequencing.
There are countless log blog posts out there about the benefits of good logging, how to log well, and how much to log. Going through them all can be a real log blog slog. Wouldn't it be cool if you could log like this:logger.info("Something happened!", job=job.id, user=user.id) and get an easily searchable output.
Caffeine is a stimulant that can induce alertness in certain individuals when consumed at an appropriate quantity. Caffeine is often obtained by ingesting caffeine-containing solutions. However, no protocol for obtaining caffeine from dehydrated, roasted beans using materials typically available in a Philadelphia office has been described in the published literature.
Alex’s Lemonade Stand Foundation (ALSF) staunchly believes that stronger scientific sharing practices will accelerate the pace of discovery and finding cures for children with cancer. Robust sharing improves reproducibility, minimizes redundant studies and maximizes our return on research investment.
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.
This year was a big one for the CCDL. In our mission to empower pediatric cancer experts poised for big discoveries with the knowledge, data and methods to reach them we launched a software product, developed and delivered training workshops on single-cell and bulk RNA-seq analysis, and hired our data science team among other milestones.
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.
Our particular process is designed to source opportunities from our team members and external stakeholders, convert those opportunities into a set of potential goals, and then select the goals that we expect will most advance our mission.
The ability to restore scroll position is often critical for website usability. It helps users keep the flow of navigation when going back and forth between different pages. Most modern browsers take care of restoring the scroll position automatically, but it doesn’t always work for Single Page Applications where the content is generated on the client’s side, often asynchronously.
Carnegie Mellon University Libraries is partnering with the Childhood Cancer Data Lab (CCDL), founded by Alex’s Lemonade Stand Foundation, to host a Data Analysis workshop using CCDL materials.
The CCDL will have a team of scientists at the American Association for Cancer Research 2020 Annual Meeting in sunny San Diego! Our team members are excited to talk to researchers studying pediatric cancer at Booth 1601.
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.
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!
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).
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.
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.
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.
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
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.
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.
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.
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.
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.
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!
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.
'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.
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.
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?
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.
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.
When the Data Lab launched the Single-cell Pediatric Cancer Atlas (ScPCA) Portal in 2022, we knew it was only the beginning! We started by making data easily available for the research community and received an overwhelmingly positive response. But we know firsthand from training hundreds of pediatric cancer researchers in analysis that making data available is just the first step. We’re increasing the impact of the Portal by listening to the growing ScPCA community. Now more researchers can contribute datasets, new features are continuously being developed, and we started an open, collaborative project to further explore the available data! Here’s a look back at how we’ve enhanced the ScPCA Portal in 2024.
Launching the Open Single-cell Pediatric Cancer Atlas (OpenScPCA) project in April 2024 was a highlight of our year! This community-driven initiative aims to analyze data from the ScPCA Portal, which currently holds 700 samples from over 55 pediatric cancer types. The project is a step forward in advancing our knowledge of pediatric cancers through single-cell analysis, and we're excited to expand OpenScPCA in 2025! To that end, we're reflecting on some of our recent accomplishments and how we can keep that momentum going into next year.
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