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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

Quality Control in Sequencing Experiments https://tess.elixir-europe.org/materials/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 those who are running sequencing facilities. Quality affairs 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

Viewing 3D Structures with Deep View https://tess.elixir-europe.org/materials/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 structures. It will also show you how to make impressive molecular graphics for your reports or posters. 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

Extracting biological information from gene lists https://tess.elixir-europe.org/materials/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 biological themes which turn up in the lists. This course looks at the various software packages, databases and statistical methods which may be of use in performing such an analysis. As well as being a practical guide to performing these types of analysis the course will also look at the types of artefacts and bias which can lead to false conclusions about functionality and will look at the appropriate ways to both run the analysis and present the results for publication. 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

Analysing bisulfite methylation sequencing data https://tess.elixir-europe.org/materials/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 the whole analysis pipeline, starting from raw sequence data and covering QC, visualisation, quantitation and differential methylation analysis. 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

RNA-Seq Analysis https://tess.elixir-europe.org/materials/rna-seq-analysis-d7e62d71-a253-4168-8b5d-6838a2384978 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 analysis and is then followed by a long hands-on practical session which runs though the entire RNA-Seq analysis pipeline from raw fastq files to a list of differentially expressed candidate genes. 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

Scientific Figure Design https://tess.elixir-europe.org/materials/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 compositing and editing of final figures. The course will use a number of different open source software packages and is illustrated with a number of example figures adapted from common analysis tools. Data visualisation 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

An Introduction to Unix https://tess.elixir-europe.org/materials/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 practical introduction to working in this environment. Internally we link this course to a more specific course illustrating the use of our internal cluster environment and this part of the course could be adapted for other sites with different compute infrastructure. 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

Plotting complex figures with R https://tess.elixir-europe.org/materials/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 of R - enough to load and do basic manipulation of datasets. 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

Advanced R https://tess.elixir-europe.org/materials/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 generate complete analysis reports. 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

Introduction to R https://tess.elixir-europe.org/materials/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 on entering and manipulating data in R and producing simple graphs. A few functions for basic statistics will be briefly introduced, but statistical functions will not be covered in detail. Software engineering R programming, Babraham Institute
Learning to Program with Perl

This course aims to introduce the basic features of the Perl language. At the end you should have everything you need to write moderately complicated programs, and enough pointers to other resources to get you started on bigger projects. The course tries to provide a grounding in the basic theory...

Keywords: perl, Babraham Institute

Learning to Program with Perl https://tess.elixir-europe.org/materials/learning-to-program-with-perl This course aims to introduce the basic features of the Perl language. At the end you should have everything you need to write moderately complicated programs, and enough pointers to other resources to get you started on bigger projects. The course tries to provide a grounding in the basic theory you'll need to write programs in any language as well as an appreciation for the right way to do things in Perl. 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 annotated genome and to quantitate and filter your data to let...

Scientific topics: Sequence alignment

Keywords: Babraham Institute

Analysing Mapped Sequence Data with SeqMonk https://tess.elixir-europe.org/materials/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 annotated genome and to quantitate and filter your data to let you identify regions of interest. It is a friendly way to explore and analysis very large datasets. This course provides an introduction to the main features of SeqMonk and will run through the anlaysis of a couple of different datasets to show what sort of analysis options it provides. Sequence alignment Babraham Institute