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The ITN has developed a library of courses covering a variety of topics relevant to cancer informatics and beyond!
The ITN has developed a library of courses covering a variety of topics relevant to cancer informatics and beyond!
Who are our courses for:
Our courses are designed for a range of audiences from those are new to data science to those who actively develop scientific software. We also have courses designed for scientific research leaders.
Our courses are designed for a range of audiences from those are new to data science to those who actively develop scientific software. We also have courses designed for scientific research leaders.
Researchers
Researchers
People who:
Do (or are starting to do) informatics research
Need resources to get started or continue to develop
Software Developers
Software Developers
People who:
Create or maintain scripts for data analysis
Create or maintain full-blown software tools that enable research
Leaders
Leaders
People who:
Lead a team
Lead a project
Act as a mentor
Make key decisions
Current Courses
Current Courses
Search for courses that are relevant for you by typing in key words in the search box or the search for each column name. Click on filter arrows next to column names to sort classes.
Check out our collection of course series - courses that build on one another for a specific topic
Reproducibility Series
Reproducibility Series
Note that all of our courses are open source, so all the source material is available on GitHub. All content is licensed with CC-BY 4.0 and therefore reusable with attribution.
Affiliated ITCR course Materials
Affiliated ITCR course Materials
CoGAPS on SciServer
CoGAPS on SciServer
This introductory course will provide a quick overview of how the Bayesian NMF algorithm, CoGAPS (Coordinated Gene Activity across Pattern Subsets), can provide new insights into single cell datasets. Through the exercises you will analyze a real dataset using the SciServer compute platform.
Links:
Links:
Introduction to pVactools
Introduction to pVactools
The course is intended for anyone seeking a better understanding of current best practices in neoantigen identification and prioritization using pVACtools. It assumes that the learner is familiar with basic biology, genetics and immunology concepts. This course will teach learners to:
Understand key concepts of immunogenomics and neoantigen identification
How to run the pVACtools software suite
How to visualize and prioritize neoantigen candidates with pVACview
Links:
Links:
Introduction to Immuno on Terra
Introduction to Immuno on Terra
This course is an introduction to the immuno workflow on Terra, which leverages a collection of modular WDL workflows for analysis of genomic sequencing data. These enable primary analysis of DNA and RNA-seq data, including for quality control, somatic and germline variant calling, expression analysis, fusion detection, HLA typing, somatic variant allele expression, and immunogenomics approaches for cancer vaccine development (including neoantigen prediction with pVACtools).
Links:
Links:
Introduction to Clinical Interpretation of Somatic Cancer Variants
Introduction to Clinical Interpretation of Somatic Cancer Variants
This course will introduce background concepts, tools, resources, and relevant standard operating procedures and guidelines for the clinical interpretation of somatic cancer variants.
The course will teach learners to:
Understand key concepts of somatic cancer variant interpretation
Introduce key SOPs and guidelines for classifying the clinical relevance and oncogenicity of somatic cancer variants
Introduce ClinGen Somatic Cancer efforts
Describe somatic variant knowledgebases
Introduce CIViC as a curation platform for somatic variant interpretation
Links:
Links:
Introduction to Open CraVat
Introduction to Open CraVat
OpenCRAVAT processes data from various popular variant file formats and offers annotations and visualizations for variants. For example answering questions like: "Given this list of variants, which are potentially pathogenic?"
This is a series of vignettes for OpenCRAVAT that show specific tasks.
They consist of multimedia content: text, images, and demo videos.
The course will teach learners to:
Create as user account on the OpenCRAVAT site
Install OpenCravat locally using an installer
Search for available annotators on the open cravat site
Upload and annotate variant files on the site
Filter annotated results for visualization
Export and Share annotation results with others
Install the OpenCRAVAT software locally using pip
Search for and Install available annotators
Annotate variant files using the CLI tools
Visualize and Summarize Results in OpenCRAVAT
Links:
Links:
GARDE
GARDE
GARDE is an open -source population health management application that identifies individuals who meet criteria for genetic testing. It is funded by several grants from the National Cancer Institute.
This course will teach learners:
About GARDE and how it works
What needs to be done to install and configure GARDE in a new organization
How to operate GARDE to identify individuals who meet guideline criteria
Links:
Links:
Additional Helpful Resources
Additional Helpful Resources
IntroductioN to R PRogramming
IntroductioN to R PRogramming
Here you will find all the resources to a course taught through Johns Hopkins: https://jhudatascience.org/intro_to_r/
Recordings of past lectures can be found at the bottom of this page: https://jhudatascience.org/intro_to_r/resources.html
Open Case Studies (OCS) for Intermediate R Programming and Statistics
Open Case Studies (OCS) for Intermediate R Programming and Statistics
https://www.opencasestudies.org/
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