FAIR Bioinformatics 2022

Click the links below to access full recordings of the 2022 FAIR Bioinformatics Course.

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Course Introduction

Defining Your RNA Strategy (Kelley Thomas, 2022)

Introduction to High Throughput Data Analysis (Tom Hampton, 2022)

Responsible Conduct of Research (Jane Disney, 2022)

Introduction to R Studio (Tom Hampton, 2022)

Basic R, Data Structures, Exploratory Statistics and Graphs (Tom Hampton, 2022)

Logic, Loops and Functions (Tom Hampton, 2022)

Promise and Challenges of Next-Generation Sequencing (Kelley Thomas, 2022)

Intro to Git and GitHub

Getting Comfortable with UNIX Server Environments (Part I)

Getting Comfortable with UNIX Server Environments (Part II)

Intro to Bulk RNA-seq: FASTQ to Gene-Level Counts

Collaborative Open Research

Quantification with Salmon

Gene ID Conversion in R

Exploratory Data Analysis and Normalization of Transcriptomic Data

edgeR and Differential Gene Expression

Over-Representation Analysis in R

Analyzing Contingency Tables

Over-representation analysis: Gene Set Enrichment

Online Tools for Gene Set and Pathway Analysis

How Data Drives Translational Medicine

Introduction to Group Exercise

Group Presentations

Machine Learning: Intro to Experimental Design

Exercises Using Plier

Introduction to Machine Learning Concepts

How Data Reuse is Revolutionizing Biomedical Research

Findable, Accessible Interoperable & Reusable in the Biomedical Context

Tools to Access Publicly Available Transcriptomic Databases

Scientific Rigor and Reproducibility (Part I)

Scientific Rigor and Reproducibility (Part II)

Data Cleaning and Merging Multiple Data Sets

Integrating the Library and the Institutional Repository to Share and Reuse Data

Linear Models

Batch Effects

Workflows for the Integration of Human and Mouse Multi-omics Data

PCA Lecture

Factors That Make Transcriptomic Data Difficult to Reproduce

Introduction to ggplot

Data Visualization with R: Histograms, Kernel Density and Violin Plots

Statistical Models

ComplexHeatmap

PCA Plots with FactoExtra

Pirate Plots and Corrplots

R Markdown and R Notebook

Writing a Data Management Plan

Reanalysis of Publicly Available Data on Shiny Web Server

Public Repositories for Omics Data

Sharing Metadata: Annotate Your Experiment

Intro to the Human Microbiome

Running QIIME2

Single Cell Analysis in R (Part I)

Single Cell Analysis in R (Part II)

Single Cell Analysis in R (Part III)

Reviewing DADA2 Statistics

Taxonomic Assessment

Assessing Beta Diversity

Increasing the Reproducibility and Rigor of Single-cell RNA-seq Through the Use of Statistics and Data Science

File Permissions and Installation Tools

Shell Variables, Wildcards, Logic and Loops

Using UNIX Pipes and Commands to Process Raw Fastq Files

Final Projects