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12 materials found

Authors: Simon Andrews 

Quality Control in Sequencing Experiments

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...

Scientific topics: Quality affairs

Keywords: Babraham Institute

Viewing 3D Structures with Deep View

Many proteins have had their structures experimentally determined, and an examination of these structures can provide valuable insights into the function of these molecules. This course will show you how to use the free Deep View software to view and analyse both single and multiple protein...

Scientific topics: Protein structure analysis

Extracting biological information from gene lists

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...

Keywords: Functional analysis, Gene lists, Babraham Institute

Analysing bisulfite methylation sequencing data

This course builds on the core skills introduced in the Introduction to R, Introduction to Unix and Introduction to SeqMonk courses to provide a more in depth look at the analysis of bisulphite sequencing data. The course is a mix of theoretical lectures and hands on practicals which go through...

Scientific topics: DNA methylation

RNA-Seq Analysis

This course builds on the core skills introduced in the Introduction to R, Introduction to Unix and Introduction to SeqMonk courses to provide a more in depth look at the analysis of RNA-Seq data. The course starts with a comprehensive lecture covering the theory of RNA-Seq data generation and...

Scientific topics: RNA-Seq

Scientific Figure Design

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...

Scientific topics: Data visualisation

Keywords: Figure design, Babraham Institute

An Introduction to Unix

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...

Keywords: Unix, Babraham Institute

Plotting complex figures with R

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...

Keywords: Graph plotting, R Programming, Babraham Institute

Advanced R

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...

Keywords: R programming, Babraham Institute

Introduction to R

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...

Scientific topics: Software engineering

Keywords: R programming, Babraham Institute

Learning to Program with Perl

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...

Keywords: perl, Babraham Institute

Analysing Mapped Sequence Data with SeqMonk

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...

Scientific topics: Sequence alignment

Keywords: Babraham Institute