Common Fund Data Ecosystem Training
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Common Fund Data Ecosystem Training
Home
Common Fund Tools
Common Fund Tools
Common Fund Tools
CFDE Portal
CFDE Portal
Overview
Human Microbiome Project Use Case
Human Microbiome Project Use Case
Using the CFDE Search Portal to Find Files
Create a CAVATICA Account
Adding Data to CAVATICA with DRS IDs
Kids First
Kids First
KF Portal Overview
Portal Setup
Portal Setup
The Setup
Register for KF
Register for Cavatica
Connecting Accounts
Accessing Data
Exploring Data
Exploring Data
Explore
Filter
Plots
Reset
Advanced Queries
Advanced Queries
Advanced Queries
Ands & Ors
Joint Queries
Checking Queries
Saving Queries
Push to Cavatica
Download Data
Download Data
Data Download Options
Data Download via KF Portal
Data Download via Cavatica
Upload Data
IDG Tutorials
Cloud Platforms
Cloud Platforms
Overview
Intro to AWS
Intro to AWS
AWS Overview
Setting up an AWS Instance
Connecting to your Instance
Using the Screen Command
Terminating an Instance
Intro to GCP
Intro to GCP
GCP Overview
Setting up GCP account
Setting up a GCP Instance
Example 1-BLAST Analysis
Example 2-Download SRA Data
Intro to Terra
Intro to Terra
Terra Overview
How does Terra work
Setting up a Terra account
Navigating Terra Workspaces
Running workflows in Terra
Custom Workflows
Let's talk about cloud costs
Bioinformatic Analyses
Bioinformatic Analyses
Overview
Command line BLAST
Command line BLAST
BLAST Overview
BLAST Search Video Walk-through
Install BLAST
How to Run a BLAST Search
Simulate Illumina Reads
GWAS in the Cloud
GWAS in the Cloud
GWAS Tutorial Overview
What is GWAS?
Set up an AWS Instance
download accessAWS
Plink install
Vcftools install
Install R and RStudio
Analyze
Manhattan Plots
Terminate AWS
RNA-Seq on Cavatica
RNA-Seq on Cavatica
RNA-Seq Tutorial Overview
An Introduction to RNA-Seq
Selecting a Kids First Cancer Cohort
Cavatica - View, Filter, Tag and Download
Setup DESeq2 Public App
Phenotype File and Upload to Cavatica
Analysis with DESeq2 Public App
Analysis using Data Cruncher
Incorporating GTEx Data in Kids First Analyses
General Tools
General Tools
Overview
Conda
Conda
Conda Overview
What is conda?
Using conda environments
Let's practice!
What else can we use Conda for?
Set up Conda on your computer
R for RNA Seq
R for RNA Seq
Overview
Introduction
Import Data
Visualize Data
Wrangle Data
Wrap-up
Snakemake
Snakemake
Snakemake Overview
Introduction
Set Up
The Snakefile
Decorating the Snakefile
Continue Decorating
Run the whole pipeline!
Example Snakefile
UNIX
UNIX
Overview
Introduction
Navigate
Read
Work
Find
Redirect
Appendix
Web Development
Web Development
Overview
Mkdocs
Jekyll
Sphinx
Javascript
Javascript
Enabling User Choices with Javascript
Demo Javascript
Demo Javascript Rendered
Release Notes
Release Notes
Latest Release
April 2022 Release
February 2022 Release
December 2021 Release
February 2021 Release
December 2020 Release
October 2020 Release
Workshop History
Website Style Guide
Website navigation
General tutorial text style guide
Tutorial components
Tutorial recordings style guide
Binder style guide
Practice Github repo style guide
Release Plan
Template
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