External Training Courses

Training from External Providers

We have compiled this link of recommended materials from other providers, and materials developed in previous roles.

Youtube Playlists

• Simon Cockell Lockdown learning
• Babraham Bioinformatics Bitesize videos
• Rafael Irizarray
• Ben Langmead - Algorithms for DNA Sequencing
• Bioconductor playlists
• Roger Peng - Exploratory Data Analysis

Reproducible Research / Data Management

Materials

• Reproducible Research Data and Project Management in R
• The Data Organisation Tutorial by Karl Broman
• The Quartz guide to bad data
• Three common bad practices in sharing tables and spreadsheets and how to avoid them
• Biologists: this is why bioinformaticians hate you…

Videos

• Keith Baggerly lecture on reproducible research
• Florian Markowetz - Five Selfish Reasons to Work Reproducibly
• Kirstie Whitaker - Show your working

Unix / Command Line

• Babraham Bioinformatics
• Software Carpentry
• CRUK Command Line for Genomics

RNA-seq

Course Materials / workflows

• University of York Differential Gene Expression Tutorial
• Harvard Bioinformatics Core Differential gene expression
• Babraham Bioinformatics
• DESeq2 workflow from the package authors
• RNA-seq with limma and edgeR

Videos

• RPKM / FPKM explained

Version control / git and github

Course Materials

• Software Carpentry git Lessons
• Github Guides
• Friendly Github Intro (Kirstie Whitaker)

Videos

• Introducing version control with Git and Github

ChiP-seq / ATAC-seq

• Harvard Bioinformatics Core ChIP-seq training
• Rockefeller Bioinformatics
• Rockefeller Bioinformatics
• Babraham Bioinformatis

Single-cell RNA-seq

Course Materials

• Orchestrating Single-Cell Analysis with Bioconductor
• Analysis of single cell RNA-seq data - Sanger
• Analysis of single cell RNA-seq data - Harvard Bioinformatics Core
• 10X analysis - Babraham Bioinformatics

Videos

• Analysis of single cell RNA-seq data - Day 1
• Analysis of single cell RNA-seq data - Day 2

Cancer Genomics

• CRUK Bioinformatics Summer School
• TCGA workflow using Bioconductor

Functional Genomics (RNA- and ChIP-seq)

• CRUK Autumn School

Epigenetics

• University of Bradford
• Bioconductor workflow for analysing methylation array data

Proteomics

• Mass spectrometry and proteomics data analysis

Python Programming

• Software Carpentry Programming with Python
• Solving biological problems with Python

Experimental Design

• CRUK course on Experimental Design

Microarray Analysis

• End-to-end workflow for Affymetrix
• CRUK course on microarray analysis

Shiny (R)

• CRUK course on Shiny for Bioinformatics

Docker

• CRUK course on using Docker

Statistics in R

• CRUK Linear Models course
• Babraham Bioinformatics Statistics in R

Scientific Figure Design

• Babraham Bioinformatics

Training Portals

• Galaxy Training Network
• GOBLET training portal