Five PowerPoint presentations and an Excel worksheet for a Train the Trainer course developed by Chris Taylor while at the Earlham Institute working for the National Institutes of Science's Bioinformatics and Biomathematics Training hub. The five slide decks cover pedagogical theory, trainer...

This is basically the EBI RNA-seq course bundled up in a Docker container using LXDE via TightVNC to provide a graphical environment. The material has been repackaged to use an Ipython Notebook as the learning environment which can be annotated by the learner.

Welcome to the IFR Dockerised version of the Welsh Genepark's

Introduction to Command-line NGS Analysis course!

The original materials belong to Wesh Genepark and the original

materials and software can be found here.

This...

Welcome to the IFR Dockerised version of the Welsh Genepark's

Introduction to Command-line NGS Analysis course!

The original materials belong to Welsh Genepark and the original

materials and software can be found here.

This...

1.Introduction to data analysis - course overview (lecture)

2.Introduction to networks (lecture)

BioLayout Express3D - background and benefits (lecture)

BioLayout Express3D – getting started 1 (Practical Session)

BioLayout Express3D – getting started 2 (Practical...

Introduction

Many Views of A Pathway(Lecture)

Pathway Models & Pathway Types (Lecture)

Sources of ‘Pathway Data’ (Lecture)

Issues (Lecture)

SBGN (Lecture)

mEPN (Lecture)

Practical Session: Pathway to Pathway Construction - yED(1)

Practical...

Introduction

Introduction to Data Summary & Types of data

Continuous Data – Measures of Location

Continuous Data – Measures of Spread & Accuracy

Continuous Data with Skewed or Odd Distributions – Measures of Spread

Choosing Appropriate Summary Statistics...

Introduction

Hypothesis Testing

Choosing Between Parametric & Non-Parametric Tests

T-Test for Comparing Two Groups

T-Test – Interpreting Software Output

Paired T-Test

Mann-Whitney U-Test to Compare Two Groups When Data Are Not Normally Distributed

8....

Introduction

One-Way Analysis of Variance (ANOVA) Recap

Two-Way ANOVA - Assessing Two Effects in Same Model

Two-Way ANOVA - Allowing for Structure in The Data

Paired T-Test Using Two-Way ANOVA & ANOVA With More Effects

Regression Recap

General Linear...

Introduction

Potential Analysis Approaches

Mixed Model Analysis

Covariance Pattern Model

Example – Covariance Pattern Model

Significance Testing for Fixed Effects

Model Checking

Random Coefficients (Slopes) Models

Example – Random Coefficients...

Power analysis is a method to estimate the samples sizes needed to detect statistical effects with high probability. This course provides an introduction to the basic principles of power analysis and goes through the variables for power calculation. It also addresses the issues associated with...

Statistics are an important part of most modern studies and being able to effectively use a statistics package can help you to understand your results. This course provides an introduction to statistics illustrated though the use of the friendly SPSS package.

**Course Content**

*...

GraphPad Prism is a powerful and friendly package which allows you to plot and analyse your data. This course acts not only as an introduction to Prism, but also goes through the basic statistical knowledge which should allow you to make the most of your data.

**Course Content**

*...

Increasing amounts of bioinformatics work is done in a command line unix environment. Most large scale processing applications are written for unix and most large scale compute environments are also based on this.

This course provides an introduction to the concepts of unix and provides a...

R is a popular language and environment that allows powerful and fast manipulation of data, offering many statistical and graphical options. This course aims to introduce R as a tool for statistics and graphics, with the main aim being to become comfortable with the R environment. It will focus...

For a long time Perl has been a popular language among those programming for the first time. Although it is a powerful language many of its features mean make it especially suited to first time programmers as it reduces the complexity found in many other languages. Perl is also one of the world's...

SeqMonk is a program which can analyse large data sets of mapped genomic positions. It is most commonly used to work with data coming from high-throughput sequencing pipelines.

The program allows you to view your reads against an...

**UNIX** is the most commonly used operating system in bioinformatics. Increasingly, the raw output of biological research exists as in silico data, usually in the form of large text files. Unix is particularly suited to work with such files and has several powerful (and flexible) commands that...

## Overview

Python is a flexible programming language that is becoming increasingly popular for scientific computing. The course is is split into 12 modules and runs over two half days. At the end of each module there a number of exercises to help solidify the learning. By the end of...

## Overview

R is a programming language and associated environment developed for statistical computing and data analysis. It provides many powerful tools for statistics, data visualisation and bioinformatics.

## Learning outcomes

- What R is suitable for.
- How to use R...

## Overview

Perl is a programming language for getting your job done. It is designed to make the easy jobs easy, without making the hard jobs impossible. Perl is also well known for BioPerl, a collection of modules which greatly simplify complicated bioinformatics tasks.

Learning...

## Overview

We make extensive use of both light and electron microscopy in our research. The aquisition of images by a microscope is only the beginning of the process of extracting meaningful and useful information from those images. As well as extracting information, it's...