Common Fund Data Ecosystem Training
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Common Fund Data Ecosystem Training
Home
Bioinformatics Skills
Bioinformatics Skills
Overview
Kids First Tutorials
Kids First Tutorials
KF Portal Overview
Portal Setup And Permissions
Portal Setup And Permissions
The Setup
Register for the Kids First DRC Portal
Register for Cavatica
Connecting Accounts
Accessing Data
Exploring Data in the KF Portal
Exploring Data in the KF Portal
Explore
Filter
Plots
Reset
Advanced KF Portal Queries
Advanced KF Portal Queries
Advanced Queries
Ands & Ors
Joint Queries
Checking Queries
Push to Cavatica
Download Data
Download Data
Data Download Options
Data Download via KF Portal
Data Download via Cavatica
CFDE Portal Tutorials
CFDE Portal Tutorials
CFDE Portal Overview
Use Case 1
Use Case 1
Cohort Selection for Blood Cancer
Blood Datasets from CF Program Portals
Use Case 2
Use Case 2
Multi-omics Data Discovery for Movement-Related Disorders
Movement Disorders Datasets in CF Program Portals
Set up Conda Computing Environment
Introduction to Amazon Web Services
Introduction to Amazon Web Services
Amazon Web Services Overview
Setting up an AWS instance video walk-through
Setting up an AWS instance
Connect to your Instance
Command Line BLAST
Command Line BLAST
BLAST Overview
BLAST search tutorial walk-through
Install BLAST
How to run a BLAST search
GWAS in the Cloud
GWAS in the Cloud
GWAS Tutorial Overview
What is GWAS?
Set up an AWS Instance
Download Data & Install Helper Utilities
Install PLINK
Install VCFtools
Install R and RStudio
Analyze
Manhattan Plots
Terminate AWS
Snakemake Workflow Management
Snakemake Workflow Management
Snakemake Overview
Introduction
Set Up
The Snakefile
Decorating the Snakefile
Continue Decorating
Run the whole pipeline!
Example Snakefile
Cheat Sheets
Cheat Sheets
Overview
Bash and nano commands
Conda commands
Snakemake commands
Web Development
Web Development
Overview
Rendering a GitHub Website Locally with Jekyll
Rendering a GitHub Website Locally with Sphinx
Rendering a GitHub Website Locally with MkDocs
Enabling User Choices with Javascript
CFDE Internal Training
CFDE Internal Training
Overview
Website Style Guide
Website Style Guide
Contributing to the nih-cfde Training and Engagement website
Website navigation
General tutorial text style guide
Tutorial components
Tutorial recordings style guide
Pangeo binder style guide
Practice Github repo style guide
Editing MkDocs Websites with cfde-bot
Identifying MIME Types
Identifying MIME Types
MIME type Overview
Introduction to MIME types
Example Data Files
file
mimetype
xdg-utils
siegfried
Multi File MIME type
Unexpected Behavior
Working with Protected Branches
Release Notes
Release Notes
CFDE Training Release
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