Book Name Description Topics

Adv Reproducibility in Cancer Informatics (github)

This course the second course in a two part series that discusses reproducibility in the context of cancer informatics.

python, r, reproducibility, version-control

AI for software (github)

DaSL’s course on AI skills for software development and programming

artificial-intelligence, chatbot, course, learn-ai, llm, llms, software-learning

AnVIL: Epigenetics Intro (github)

An introductory activity for epigenetics, or the idea of “nature versus nurture” in genetics. Learners use the UCSC Genome Browser.

anvil, course, epigenetics, human-genomes, module, ucsc-browser

AnVIL: Getting Started (github)

A guide for getting started using AnVIL

anvil, cloud-computing

AnVIL: Instructor Guide (github)

A guide for instructors using AnVIL for workshops, lessons, or courses.

anvil, education

AnVIL Collection (github)

📚 An auto-generating collection of all materials related to the AnVIL and GDSCN projects

content-library, website

AnVIL Data Subsetting (github)

Tutorial for running the fastq_subsample WDL workflow on AnVIL!

anvil, genomics, wdl, wdl-workflow, workflow

AnVIL Demos (github)

⏱ 30-minute demos and tutorials from our live AnVIL series

anvil, cloud, cloud-computing, genomics, research

AnVIL Phylogenetic-Techniques (github)

A semester-long course on the basics of molecular phylogenetic techniques

anvil, r-programming

AnVIL SRA Data (github)

Pull Sequence Read Archive (SRA) data into AnVIL

anvil, genomics, ncbi-database, sequence-read-archive

AnVIL Template (github)

An OTTR spinoff template for creating AnVIL content

anvil, template

AnVIL Urban Genomics PCA (github)

Lab module and lectures for exploring PCA using feral pigeon populations

anvil, genomics, pca, urban-data-science

AnVIL WDLs (github)

Raw WDL workflow files for use on AnVIL and other platforms

anvil, genomics, wdl, workflows

ari (github)

:dancers: The Automated R Instructor


Baltimore Community Course (github)

Baltimore Community Data Science Course at JHSPH through partnership with SOURCE

community-outreach, course, data-science

Choosing Genomics Tools (github)

A course to help learners find resources and tools to help them process and interpret their genomic data


code review (github)

A repository with tips about code review and implementing it in a lab

codereview, fhdasl, training

Computing for Cancer Informatics (github)

The course covers the key underlying principles and concepts in computing. It covers concrete discussions of the differences between cloud and local computing. The course highlights a number of computing options and etiquette for using shared resources.

computing, informatics

conrad (github)

Client for the Microsoft Cognitive Services Text to Speech REST API (reboot of the mscstts package)

azure, r, text-to-speech, tts

DaSL Collection (github)

📚 An auto-generating library of all Data Science Lab Github-based content

content-library, website

dasl-snack-github (github)

A DaSL training “snack” covering the benefits and basics of using Git and GitHub to support your biomedical data science work.


Data-Wrangling (github)

UW Summer Institute in Statistics: Data Wrangling in R

data-science, data-wrangling, r-programming, r-stats, tidyverse

DataTrail: 12 package (github)

How to Create an R package Course

data-science, package-development, r-package

DataTrail: DataTrail (github)

The re-organized DataTrail curriculum


DataTrail: DataTrail Guides (github)

Guides for how to launch a DataTrail program


DataTrail: rgoogleclassroom (github)

API wrapper for Google Classroom and a bit of Google Forms API too


DataTrail: scn (github)

:school_satchel: The swirl Course Network - A Repository for swirl Courses


Documentation and Usability (github)

A course to cover the basics of creating documentation and tutorials to maximize the usability of informatics tools

documentation, software-development

Ethical Data Handling for Cancer Research (github)

This course is designed to help researchers and investigators understand the key principles of data management from an ethics, privacy, security, usability and discoverability perspective.

data, ethics, privacy, research, security

FH Cluster Guide (github)

This course introduces users to the Fred Hutch Cluster. It will lead users through account creation, using the terminal, connecting to the cluster, submitting jobs, and transferring files. Available in both web and Leanpub formats.

command-line, computing-cluster, course, fredhutch, hpcc

FH Cluster201 (github)

An emerging course for effective use of FH Computing.


FH letterhead (github)

A LaTeX template for Fred Hutch letterhead

latex, letterhead, template

FH WDL101 Cromwell (github)

An introduction to using Cromwell and WDL at the Fred Hutch

course, fredhutch, wdl

FH WDL102 Workflows (github)

Info about designing, optimizing and deploying your own WDL workflows

course, fredhutch, openwdl, wdl, workflows

GDSCN: SARS Galaxy on AnVIL (github)

Lab module and lectures for variant detection in SARS-CoV-2 using Galaxy

anvil, gdscn, genomics, module, sars-cov-2, variant-detection

GDSCN: Statistics for Genomics Differential Expression (github)

A set of lab modules for an introduction to differential gene expression

anvil, cloud-computing, gdscn, gene-expression

GDSCN: Statistics for Genomics PCA (github)

A set of lab modules for PCA analysis

anvil, gdscn, genomics

GDSCN: Statistics for Genomics RNA-seq (github)

[WORK IN PROGRESS] A set of lab modules for RNA-seq analysis


GDSCN: Statistics for Genomics scRNA-seq (github)

A set of lab modules for single cell RNA-seq analysis

anvil, gdscn, rna-seq, scrna-seq

GDSCN: swirl (github)

Lab exercise: learn basic R programming through interactive swirl lessons

gdscn, swirl

GDSCN SARS RStudio on AnVIL (github)

Lab module and lectures for identifying phylogenetic history of SARS variants using R

anvil, gdscn, phylogenetic-analysis, sars-cov-2

Informatics Research Leadership (github)

Guidance on supporting multidisciplinary teams in cancer informatics.

diversity, informatics, leadership

intro to r (github)

A 2-week introduction to R programming course, with a focus on public health datasets

beginner, beginner-friendly, beginner-programming, course, public-health, r-programming, tidyverse (github)

source code for the JHU Data Science Lab website


NIH Data Sharing (github)

Learn about the new NIH data sharing policy, places where you might want to share your particular kind of data, and how to deal with possible challenges associated with the policy.

data-management, data-sharing, grant-proposals, nih

OTTR Template (github)

OTTR: Open-source Tools for Training Resources. This is template repository for creating online courses to be published on multiple platforms. See here: for a rendered version.

education, online-learning, open-source

OTTR Template Website (github)

Template to create websites with checks for broken urls and spelling, as well as automated rendering. This is an offshoot of the OTTR_Template (


ottr-website (github)

The website for OTTR


ottrpal (github)

Tools for converting OTTR courses into Leanpub or Coursera courses :otter:


Overleaf and LaTeX for Scientific Articles (github)

The course covers basic information about why LaTeX can be useful, how to get started in Overleaf using LaTeX with a template, how to work with a team on Overleaf, and what to do when you encounter problems.

latex, overleaf, scientific-publications

personas (github)

Where RDI curates the DaSL Data Science Personas

data-science, personas, training

Reproducibility in Cancer Informatics (github)

This course discusses reproducibility and replicability in the context of cancer informatics.

data-science, informatics, python, r, reproducibility

SeattleStatSummer R (github)

A 4-day introduction to R programming, focused on Fred Hutch Research Interns

beginner, beginner-friendly, data-analysis, data-science, introduction-to-programming, r-programming, tidyverse

text2speech (github)

Text to Speech

speech-synthesis, text-to-speech, tts, voice

tidyversecourse (github)

Tidyverse Skills for Data Science in R

r, tidyverse

uplifthub website (github)

Website for the Uplift Hub


Using Leanpub (github)

A gentle introduction to Leanpub

education, leanpub

This page was last updated on 2023-09-23 03:06:42