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...

An LXDE Rstudio with pre-loaded Bioconductor tools for rna-seq DE analysis & visualisation

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. Phylogenetics & Phylogeography (lecture-part 1)

2. Phylogenetics & Phylogeography (lecture-part 2)

3. Phylogenetics & Phylogeography (lecture-part 3)

4. Phylogenetics & Phylogeography (lecture-part 4)

5. Phylogenetics & Phylogeography (lecture-part 5)

6....

1. Molecular epidemiology - practical 1

2. Molecular epidemiology - practical 1 review

3. Molecular epidemiology - practical 2 part 1

4. Molecular epidemiology - practical 2 part 2

5. Molecular epidemiology - practical 2 review

6. Molecular epidemiology - practical 3 part 1

7....

1. Phylogenetic analysis of pathogens (lecture - part1)

2. Phylogenetic analysis of pathogens (lecture - part2)

3. Phylogenetic analysis of pathogens (lecture - part3)

4. Phylogenetic analysis of pathogens (lecture - part4)

5. Phylogenetic analysis of pathogens (lecture - part5)

6....

1. Introduction

2. Many Views of A Pathway(Lecture)

3. Pathway Models & Pathway Types (Lecture)

4. Sources of ‘Pathway Data’ (Lecture)

5. Issues (Lecture)

6. SBGN (Lecture)

7. mEPN (Lecture)

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

9. Practical...

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

2.Introduction to networks (lecture)

1. BioLayout Express3D - background and benefits (lecture)

2. BioLayout Express3D – getting started 1 (Practical Session)

3. BioLayout Express3D – getting started 2 (Practical...

1. Phylogenetics & Phylogeography Practical - Overview

2. Phylogenetics & Phylogeography Practical 1

3. Phylogenetics & Phylogeography Practical 2 - Part 1

4. Phylogenetics & Phylogeography Practical 2 - Part 2

5. Phylogenetics & Phylogeography Practical 3

6....

1. Introduction

2. Many Views of A Pathway(Lecture)

3. Pathway Models & Pathway Types (Lecture)

4. Sources of ‘Pathway Data’ (Lecture)

5. Issues (Lecture)

6. SBGN (Lecture)

7. mEPN (Lecture)

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

9. Practical...

1.Introduction

1. Data summary

2. Demo – Data Summary

3. Demo – Data Summary cont.

4. Data summary using PROC TABULATE and PROC GPLOT

5. Statistical analysis

6. Example analysis

7. Example analysis cont.1

8. Example analysis cont.2

9. Reading and manipulating...

1. A Brief Introduction to R

2. Very Basic Functions

3. Demo Data - Rivers

4. Demo Data - Rivers (Cont.)

5. Demo Data - Orange

6. Demo Data - Orange (Cont.)

7. Demo data - Anderson's Iris Data

8. Demo Data - US Judge Rating

9. Summary

1. Introduction

2. Introduction to Data Summary & Types of data

3. Continuous Data – Measures of Location

4. Continuous Data – Measures of Spread & Accuracy

5. Continuous Data with Skewed or Odd Distributions – Measures of Spread

6. Choosing Appropriate Summary Statistics...

1. Introduction

2. Hypothesis Testing

3. Choosing Between Parametric & Non-Parametric Tests

4. T-Test for Comparing Two Groups

5. T-Test – Interpreting Software Output

6. Paired T-Test

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

8....

1. Introduction

2. Achieving Statistical Significance

3. Achieving Generalisable Results

4. Avoiding Bias

5. Questions to Address When Planning

6. Examples of Experimental Designs

7. Randomised Block Design

8. Crossover & Repeated Measures Designs

9. Pilot & Proof...

1. Introduction

2. Sample Size Calculation – Basic Formula

3. Example 1

4. Calculating In Terms of ‘Difference to Detect’ & Power From Sample Size

5. Example 2

6. Different Numbers Per Group

7. Different Variances for Groups

8. Binary Data

9. Allowing for...

1. Introduction

2. One-Way Analysis of Variance (ANOVA) Recap

3. Two-Way ANOVA - Assessing Two Effects in Same Model

4. Two-Way ANOVA - Allowing for Structure in The Data

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

6. Regression Recap

7. General Linear...

1. Introduction

2. What Are Mixed Models?

3. Potential Advantages of Mixed Models

4. Historical Perspective

5. Example 1: Biological & Technical Replicates

6. Example 2: Rabbit Inspiration Time – Sources of Variation

7. Non-Normal Data

8. Example 3: Non-normal data

9....

1. Introduction

2. Potential Analysis Approaches

3. Mixed Model Analysis

4. Covariance Pattern Model

5. Example – Covariance Pattern Model

6. Significance Testing for Fixed Effects

7. Model Checking

8. Random Coefficients (Slopes) Models

9. Example – Random Coefficients...

This course looks at the different ways in which sequencing based studies can fail and the options for visualisation and QC which allow you to identify and diagnose these failures at an early stage. It is designed to be of use to anyone who is using sequencing as part of their research, not just...

Many experimental designs end up producing lists of hits, usually based around genes or transcripts. Sometimes these lists are small enough that they can be examined individually, but often it is useful to do a more structured functional analysis to try to automatically determine any interesting...

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

*...

This course provides a practical guide to producing figures for use in reports and publications. It is a wide ranging course which looks at how to design figures to clearly and fairly represent your data, the practical aspects of graph creation, the allowable manipulation of bitmap images and...

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...

Ggplot is the most popular plotting extension to R and replicates many of the graph types found in the core plotting libraries. This course provides an introduction to the ggplot2 libraries and gives a practical guide for how to use these to create different types of graphs.

**Course...

This course is a comprehensive guide to the use of the built in R plotting functionality to construct everything from customised simple plots to complex multi-layered figures. It follows on from the material in our introductory R course and participants are expected to have a basic understanding...