Research Resources

A curated list of resources for pediatric cancer researchers ranging from lectures to repositories.

Cancer Research Education

Virtual Childhood Cancer Speaker Series

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Free educational presentations by leading experts in the field of pediatric cancer research.

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The DF/HCC Connect: Science seminar series

A virtual seminar series featuring leaders in cancer biology, immuno-oncology and more.

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Science of Childhood Cancer Virtual Lecture Series

St. Jude Children’s Research Hospital holds free weekly virtual lectures featuring a different expert speaker during the spring and fall.

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SITC-NCI Computations Immuno-oncology Webinar Series

Free virtual events to advance your training in computational immuno-oncology.

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Data Science Tools and Education

Childhood Cancer Data Lab Projects

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Free, open source tools and resources that make data and analysis widely available.

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Data science training workshops

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Workshops that teach childhood cancer researchers data science skills to better understand their data and to collaborate more effectively.

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Comprehensive Learning Resources

The Carpentries

Training workshops and self-paced free materials that teach data science, coding, and bioinformatics  skills. Learn about the Carpentries

Data CarpentrySoftware Carpentry

Harvard Chan Bioinformatics Core (HBC) Training Program

Bioinformatics training workshops for getting started with analyzing high-throughput data.

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Informatics Technology for Cancer Research (ITCR)

Learning opportunities that support cancer informatics and data science training. Learn about ITCR

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Learning Bioinformatics at Home

Information compiled by the Harvard Informatics group on learning to use bioinformatics tools on your own. 

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Data and Resource Sharing

Childhood Cancer Repository

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A repository which banks and distributes validated cell lines and patient-derived xenografts.

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Childhood Cancer Research Resources (CCRR) Portal

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A platform to enable the discovery and sharing of resources such as cell lines, datasets, and plasmids.

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Childhood Cancer Data Catalog

An inventory of pediatric oncology data resources. The catalog is part of NCI’s Childhood Cancer Data Initiative (CCDI).

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Cooperative Human Tissue Network (CHTN)

NCI supported resource for obtaining biospecimens for research. 

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Coriell Biobank

Biological samples from common diseases. 

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Genomic Data Commons

A repository and knowledge base enabling data sharing across cancer genomic studies.

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St. Jude Cloud

Cloud-based genomic resource for pediatric cancer data.

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UCSC Treehouse Public Data

A compendium of RNA gene expression data available for download and visualization.

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Kids First Data Resource Center

Large-scale collection of pediatric cancer data made available through a portal. Learn more

CAVATICA

Cloud-based resource for sharing data, results, and workflows.

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PedcBioPortal

Cloud-based platform linking data visualization to available biospecimens.

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Git

GitHub Learning Lab

Get started with GitHub, a platform for software development, version control, collaboration and more.

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Happy Git with R

Instructions for integrating Git and GitHub into your workflows with R.

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R Programming

Data Visualization - A Practical Introduction

Introduction to the ideas and the methods of data visualization.

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Getting Used to R, RStudio, and R Markdown

A book to help beginners get started with R. 

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ggplot2: Elegant Graphics for Data Analysis

A book on the basics of ggplot2 and the graphics it uses.

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R for Data Science

The website for a book that teaches data science with R. 

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R for Data Science Online Learning Community

A supportive community for R learners at all skill levels.

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The R Graph Gallery

Collection of charts made with R. The reproducible code and explanations are provided.

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Riffomonas

Training workshops and tutorials for R and reproducible computational methods. 

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Swirl

A software package for R that offers self-paced learning of data science and R.

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RStudio

Open source software for data science. Learn more

RStudio Cheatsheets

Handy information for using R packages.

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R Markdown

Learn to create high quality, reproducible documentation.

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RStudio Webinars

Free webinars offering helpful advice to the data science community.

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RNA-sequencing

RNA-seqlopedia

An overview of RNA-seq and the steps involved in carrying out an experiment. 

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Single-cell RNA-sequencing

Orchestrating Single-Cell Analysis with Bioconductor

The website for a book that teaches common workflows for the analysis of single-cell data.

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Unix

Unix Bootcamp

A basic overview of essential Unix and Linux commands.

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Unix Tutorial for Beginners

A beginners guide to the Unix and Linux operating system.

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Workflow Managers

Nextflow documentation

Documentation for using the Nextflow workflow manager.

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Tips for using Nextflow

A blog post with tips and tricks on using Nextflow.

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Snakemake tutorial

A guide for using Snakemake workflow manager.

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