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

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 Phylogenetic-Techniques (github)

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

anvil, r-programming

AnVIL Template (github)

An OTTR spinoff template for creating AnVIL content

anvil, template

Baltimore Community Course (github)

Baltimore Community Data Science Course at JHSPH through partnership with SOURCE

community-outreach, course, data-science

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

computing, informatics

DaSL Collection (github)

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

content-library, website

Data-Wrangling (github)

UW Summer Institute in Statistics: Data Wrangling in R

data-science, r-programming, tidyverse

DataTrail: 00 intro (github)

Course 0: Intro to DataTrail


DataTrail: 01 chromebookintro (github)

Course 1: How To Use A Chromebook


DataTrail: 02 googlecloud (github)

Course 2: Google & Cloud

data-science, google-cloud

DataTrail: 03 fileorganization (github)

Course 3: File Organization & Projects

data-science, project-organization

DataTrail: 04 githubbasics (github)

Course 4: Github

data-science, github, version-control

DataTrail: 05 R (github)

Course 5: Introduction to R

data-science, programming, r

DataTrail: 06 datacleaning (github)

Course 6: Data cleaning and wrangling

data-science, data-tidying, data-wrangling

DataTrail: 07 dataviz (github)

Course 7: Data Visualization

data-science, data-visualization, ggplot2

DataTrail: 08 data (github)

Course 8: Getting Data

data-download, data-science, data-setup

DataTrail: 09 dataanalysis (github)

Course 9: Basics of Data Analysis

data-analysis, data-science, r

DataTrail: 10 communication (github)

Course 10: Getting a job in data science

career, career-development, communication, data-science

DataTrail: 11 dsjob (github)

Course 11: Getting a job in data science

career-development, data-science, jobsearch

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: 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

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, genomics, module

GDSCN: Statistics for Genomics Differential Expression (github)

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

anvil, cloud-computing, gene-expression

GDSCN: Statistics for Genomics PCA (github)

A set of lab modules for PCA analysis


GDSCN: Statistics for Genomics RNA-seq (github)

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


GDSCN: swirl (github)

Lab exercise: learn basic R programming through interactive swirl lessons


GDSCN SARS Phylogeny on AnVIL (github)

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


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, course, r-programming, tidyverse (github)

source code for the JHU Data Science Lab website


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


Reproducibility in Cancer Informatics (github)

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

data-science, informatics, python, r, reproducibility

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 2023-01-30 03:06:44