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...

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...

Audience

The intended audience includes any student, postdoc or RA who has an interest in bioinformatics and who intends to conduct RNA-Seq analysis on a Galaxy platform.

Overview

RNA-Seq is an immensely powerful technique that allows us to examine the presence and...

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

The Linux operating system underlies the HPC cluster at the NBI, and other clusters throughout the world. Unlike Windows and OS X, we usually interact with these systems through the command line. The course will teach the basics of Linux use.

Learning...

R is an open source programming/scripting language.

• Inspired by the programming language S.
• Useful for statistics and data science.
• Superior like commercial alternatives (over 7,000 user contributed packages at this time).
• Widely used both in academia and industry.
• Available on...

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...

Introduction to Galaxy

• Introduction to Reads Mapping
• Hands-on experience:
• Upload data on Galaxy repository
• Perform bioinformatics analysis with Galaxy
• Save data
• Visualize the results

Sequence processing Issues

General sequence quality

• 5’ base bias
• 3’ quality decline

Library diversity

• Low complexity sequence
  
• Over-amplification

Contamination

• Intrinsic to sample?
• Cross contamination? *...

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. 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. 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. 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. 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. 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...

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...

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...

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...

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....

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...

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...

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...

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

*...

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...

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. 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....

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...

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...

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.

This course follows on from the introductory course. It goes into more detail on practical guides to filtering and combining complex data sets. It also looks at other core R concepts such as looping with apply statements and using packages. Finally it looks at how to document your R analyses and...

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...

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....

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...

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...

Introduction: What are Virtual Machines?

• We introduce the concept of the virtual machine, what they can be used for and the advantages and disadvantages of using them.

Why use a Virtual machine and what is it?

• Fetching and installing the VM software

• Getting Virtualbox Book

*...

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...

Overview

Galaxy is an open, web-based platform for data intensive biomedical research. It offers an accessible, reproducible and transparent computational workbench for the biologist. This workbench is very useful in automating repeated analysis steps in the form of workflows. The...

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...

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...

Overview

Chromatin Immunoprecipiation (ChIP) allows us to identify DNA sequences bound by particular proteins. This provides a powerful way to investigate chromatin-associated proteins such as transcription factors. Recent advances in high throughput sequencing allow ChIP data...

What is HPC

• Our HPC(s)
• Submitting a job to the HPC
• Monitoring your running job
• When your job has finished
• Checking how the resources on the HPC are being used
• Submitting multiple jobs
• Best practice

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...

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...

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....

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...

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...

Complete course materials from the 2015 Python course.

Course materials from the data QC and preparation course.

Course materials from the 2015 De Novo course.

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

Complete course materials from the Ensembl Genomes course.

Complete course materials from the 2014 pathways to networks course.

Complete course materials from the 2014 GBS course.

Complete course materials from the 2014 Summer School.

Complete course materials from the 2015 GBS course.

Complete course materials from the 2014 NGS course.

Complete course materials from the 2013 Python course.

Course materials from the 2015 de novo course.

Course materials from the 2015 De Novo course.

Course materials from the 2015 de novo course.

Complete course materials from the 2014 SWC course.