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Bioinformatics Training

Bioinformatics course timetable

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Fri 12 Aug – Fri 2 Dec

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Monday 12 September

09:30
Analysis of single cell RNA-seq data (IN PERSON) (1 of 3) [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Recent technological advances have made it possible to obtain genome-wide transcriptome data from single cells using high-throughput sequencing (scRNA-seq). Even though scRNA-seq makes it possible to address problems that are intractable with bulk RNA-seq data, analysing scRNA-seq is also more challenging.

In this course we will be surveying the existing problems as well as the available computational and statistical frameworks available for the analysis of scRNA-seq.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Introduction to Python for Biologists (ONLINE LIVE TRAINING) (1 of 2) [Places] 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

This course provides a practical introduction to the writing of Python programs for the complete novice. Participants are lead through the core concepts of Python including Python syntax, data structures and reading/writing files. These are illustrated by a series of example programs. Upon completion of the course, participants will be able to write simple Python programs.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Tuesday 13 September

09:30
Introduction to R for Biologists (ONLINE) (1 of 2) [Full] 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

PLEASE BE AWARE: This event is run online, if you wish to book for the in-person version, please click here.

R is one of the leading programming languages in Data Science. It is widely used to perform statistics, machine learning, visualisations and data analyses. It is an open source programming language so all the software we will use in the course is free. This course is an introduction to R designed for participants with no programming experience. We will start from scratch by introducing how to start programming in R and progress our way and learn how to read and write to files, manipulate data and visualise it by creating different plots - all the fundamental tasks you need to get you started analysing your data. During the course we will be working with one of the most popular packages in R; tidyverse that will allow you to manipulate your data effectively and visualise it to a publication level standard.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Introduction to R for Biologists (IN PERSON) (1 of 2) [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

PLEASE BE AWARE: This event is run in-person, if you wish to book for the online version, please click here.

R is one of the leading programming languages in Data Science. It is widely used to perform statistics, machine learning, visualisations and data analyses. It is an open source programming language so all the software we will use in the course is free. This course is an introduction to R designed for participants with no programming experience. We will start from scratch by introducing how to start programming in R and progress our way and learn how to read and write to files, manipulate data and visualise it by creating different plots - all the fundamental tasks you need to get you started analysing your data. During the course we will be working with one of the most popular packages in R; tidyverse that will allow you to manipulate your data effectively and visualise it to a publication level standard.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Wednesday 14 September

09:30
Introduction to R for Biologists (ONLINE) (2 of 2) [Full] 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

PLEASE BE AWARE: This event is run online, if you wish to book for the in-person version, please click here.

R is one of the leading programming languages in Data Science. It is widely used to perform statistics, machine learning, visualisations and data analyses. It is an open source programming language so all the software we will use in the course is free. This course is an introduction to R designed for participants with no programming experience. We will start from scratch by introducing how to start programming in R and progress our way and learn how to read and write to files, manipulate data and visualise it by creating different plots - all the fundamental tasks you need to get you started analysing your data. During the course we will be working with one of the most popular packages in R; tidyverse that will allow you to manipulate your data effectively and visualise it to a publication level standard.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Introduction to R for Biologists (IN PERSON) (2 of 2) [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

PLEASE BE AWARE: This event is run in-person, if you wish to book for the online version, please click here.

R is one of the leading programming languages in Data Science. It is widely used to perform statistics, machine learning, visualisations and data analyses. It is an open source programming language so all the software we will use in the course is free. This course is an introduction to R designed for participants with no programming experience. We will start from scratch by introducing how to start programming in R and progress our way and learn how to read and write to files, manipulate data and visualise it by creating different plots - all the fundamental tasks you need to get you started analysing your data. During the course we will be working with one of the most popular packages in R; tidyverse that will allow you to manipulate your data effectively and visualise it to a publication level standard.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Thursday 15 September

09:30
Using the Ensembl Genome Browser (IN PERSON) [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

The Ensembl Project provides a comprehensive and integrated source of annotation of, mainly vertebrate, genome sequences. This workshop offers a comprehensive practical introduction to the use of the Ensembl genome browser as well as essential background information.

This course will focus on the vertebrate genomes in Ensembl, however much of what will be covered is also applicable to the non-vertebrates (plants, bacteria, fungi, metazoa and protists) in Ensembl Genomes.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Friday 16 September

09:30
Ensembl REST API workshop (IN PERSON) [Places] 09:30 - 16:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

The Ensembl project provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences.

This workshop is aimed at researchers and developers interested in exploring Ensembl beyond the website. The workshop covers how to use the Ensembl REST APIs, including understanding the major endpoints and how to write scripts to call them.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Monday 19 September

09:30
Analysis of single cell RNA-seq data (IN PERSON) (2 of 3) [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Recent technological advances have made it possible to obtain genome-wide transcriptome data from single cells using high-throughput sequencing (scRNA-seq). Even though scRNA-seq makes it possible to address problems that are intractable with bulk RNA-seq data, analysing scRNA-seq is also more challenging.

In this course we will be surveying the existing problems as well as the available computational and statistical frameworks available for the analysis of scRNA-seq.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Introduction to Python for Biologists (ONLINE LIVE TRAINING) (2 of 2) [Places] 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

This course provides a practical introduction to the writing of Python programs for the complete novice. Participants are lead through the core concepts of Python including Python syntax, data structures and reading/writing files. These are illustrated by a series of example programs. Upon completion of the course, participants will be able to write simple Python programs.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Monday 26 September

09:30
Analysis of single cell RNA-seq data (IN PERSON) (3 of 3) [Places] 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Recent technological advances have made it possible to obtain genome-wide transcriptome data from single cells using high-throughput sequencing (scRNA-seq). Even though scRNA-seq makes it possible to address problems that are intractable with bulk RNA-seq data, analysing scRNA-seq is also more challenging.

In this course we will be surveying the existing problems as well as the available computational and statistical frameworks available for the analysis of scRNA-seq.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Wednesday 28 September

09:30
Core Statistics using R (ONLINE) (1 of 3) [Places] 09:30 - 17:00 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

PLEASE BE AWARE: This event is run online, if you wish to book for the in-person version, please click here.

This award winning virtually delivered course is intended to provide a strong foundation in practical statistics and data analysis using the R software environment. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences.

There are three core goals for this course:

  1. Use R confidently for statistics and data analysis
  2. Be able to analyse datasets using standard statistical techniques
  3. Know which tests are and are not appropriate

R is an open source programming language so all of the software we will use in the course is free.

In this course, we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to linear models and power analyses. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory.

After the course you should feel confident to be able to select and implement common statistical techniques using R and moreover know when, and when not, to apply these techniques.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Core Statistics using R (IN PERSON) (1 of 3) [Places] 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

PLEASE BE AWARE: This event is run in-person, if you wish to book for the online version, please click here.

This award winning virtually delivered course is intended to provide a strong foundation in practical statistics and data analysis using the R software environment. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences.

There are three core goals for this course:

  1. Use R confidently for statistics and data analysis
  2. Be able to analyse datasets using standard statistical techniques
  3. Know which tests are and are not appropriate

R is an open source programming language so all of the software we will use in the course is free.

In this course, we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to linear models and power analyses. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory.

After the course you should feel confident to be able to select and implement common statistical techniques using R and moreover know when, and when not, to apply these techniques.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Thursday 29 September

09:30
Core Statistics using R (ONLINE) (2 of 3) [Places] 09:30 - 17:00 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

PLEASE BE AWARE: This event is run online, if you wish to book for the in-person version, please click here.

This award winning virtually delivered course is intended to provide a strong foundation in practical statistics and data analysis using the R software environment. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences.

There are three core goals for this course:

  1. Use R confidently for statistics and data analysis
  2. Be able to analyse datasets using standard statistical techniques
  3. Know which tests are and are not appropriate

R is an open source programming language so all of the software we will use in the course is free.

In this course, we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to linear models and power analyses. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory.

After the course you should feel confident to be able to select and implement common statistical techniques using R and moreover know when, and when not, to apply these techniques.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Core Statistics using R (IN PERSON) (2 of 3) [Places] 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

PLEASE BE AWARE: This event is run in-person, if you wish to book for the online version, please click here.

This award winning virtually delivered course is intended to provide a strong foundation in practical statistics and data analysis using the R software environment. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences.

There are three core goals for this course:

  1. Use R confidently for statistics and data analysis
  2. Be able to analyse datasets using standard statistical techniques
  3. Know which tests are and are not appropriate

R is an open source programming language so all of the software we will use in the course is free.

In this course, we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to linear models and power analyses. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory.

After the course you should feel confident to be able to select and implement common statistical techniques using R and moreover know when, and when not, to apply these techniques.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Friday 30 September

09:30
Core Statistics using R (ONLINE) (3 of 3) [Places] 09:30 - 17:00 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

PLEASE BE AWARE: This event is run online, if you wish to book for the in-person version, please click here.

This award winning virtually delivered course is intended to provide a strong foundation in practical statistics and data analysis using the R software environment. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences.

There are three core goals for this course:

  1. Use R confidently for statistics and data analysis
  2. Be able to analyse datasets using standard statistical techniques
  3. Know which tests are and are not appropriate

R is an open source programming language so all of the software we will use in the course is free.

In this course, we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to linear models and power analyses. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory.

After the course you should feel confident to be able to select and implement common statistical techniques using R and moreover know when, and when not, to apply these techniques.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Core Statistics using R (IN PERSON) (3 of 3) [Places] 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

PLEASE BE AWARE: This event is run in-person, if you wish to book for the online version, please click here.

This award winning virtually delivered course is intended to provide a strong foundation in practical statistics and data analysis using the R software environment. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences.

There are three core goals for this course:

  1. Use R confidently for statistics and data analysis
  2. Be able to analyse datasets using standard statistical techniques
  3. Know which tests are and are not appropriate

R is an open source programming language so all of the software we will use in the course is free.

In this course, we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to linear models and power analyses. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory.

After the course you should feel confident to be able to select and implement common statistical techniques using R and moreover know when, and when not, to apply these techniques.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Wednesday 19 October

09:30
Introduction to working with UNIX and bash (ONLINE LIVE TRAINING) (1 of 2) [Places] 09:30 - 13:00 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

Using the Linux operating system and the bash command line interface, we will demonstrate the basic structure of the UNIX operating system and how we can interact with it using a basic set of commands. Applying this, we will learn how to navigate the filesystem, manipulate text-based data and structure simple pipelines out of these commands.

Building on the techniques learnt so far, we will then construct bash scripts combining the commands and structures already learnt into more complex, reusable tools. We will look at how we can apply these scripts to common problems faced in UNIX environments such as: communicating with remote servers; managing custom software installations and integrating these tools into our simple pipelines.

This course is targeted at participants with no prior experience working with UNIX-like systems (OSX, Linux) or command line interfaces.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking here.

Thursday 20 October

09:30
Introduction to working with UNIX and bash (ONLINE LIVE TRAINING) (2 of 2) [Places] 09:30 - 13:00 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

Using the Linux operating system and the bash command line interface, we will demonstrate the basic structure of the UNIX operating system and how we can interact with it using a basic set of commands. Applying this, we will learn how to navigate the filesystem, manipulate text-based data and structure simple pipelines out of these commands.

Building on the techniques learnt so far, we will then construct bash scripts combining the commands and structures already learnt into more complex, reusable tools. We will look at how we can apply these scripts to common problems faced in UNIX environments such as: communicating with remote servers; managing custom software installations and integrating these tools into our simple pipelines.

This course is targeted at participants with no prior experience working with UNIX-like systems (OSX, Linux) or command line interfaces.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking here.

Friday 18 November

09:30
Analysis of bulk RNA-seq data (ONLINE LIVE TRAINING) (1 of 3) [Full] 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

The aim of this course is to familiarize the participants with the primary analysis of RNA-seq data.

This course starts with a brief introduction to RNA-seq and discusses quality control issues. Next, we will present the alignment step, quantification of expression and differential expression analysis. For downstream analysis we will focus on tools available through the Bioconductor project for manipulating and analysing bulk RNA-seq.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Friday 25 November

09:30
Analysis of bulk RNA-seq data (ONLINE LIVE TRAINING) (2 of 3) [Full] 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

The aim of this course is to familiarize the participants with the primary analysis of RNA-seq data.

This course starts with a brief introduction to RNA-seq and discusses quality control issues. Next, we will present the alignment step, quantification of expression and differential expression analysis. For downstream analysis we will focus on tools available through the Bioconductor project for manipulating and analysing bulk RNA-seq.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Thursday 1 December

09:30
Reproducible Research with R (ONLINE) [Places] 09:30 - 17:00 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

PLEASE BE AWARE: This event is run online, if you wish to book for the in-person version, please click here.

This course introduces concepts about reproducibility that can be used when you are programming in R. We will explore how to create notebooks - a way to integrate your R analyses into reports using Rmarkdown. The course also introduces the concept of version control. We will learn how to create a repository on GitHub and how to work together on the same project collaboratively without creating conflicting versions of files.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Reproducible Research with R (IN PERSON) [Places] 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site

PLEASE BE AWARE: This event is run in-person, if you wish to book for the online version, please click here.

This course introduces concepts about reproducibility that can be used when you are programming in R. We will explore how to create notebooks - a way to integrate your R analyses into reports using Rmarkdown. The course also introduces the concept of version control. We will learn how to create a repository on GitHub and how to work together on the same project collaboratively without creating conflicting versions of files.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Friday 2 December

09:30
Analysis of bulk RNA-seq data (ONLINE LIVE TRAINING) (3 of 3) [Full] 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

The aim of this course is to familiarize the participants with the primary analysis of RNA-seq data.

This course starts with a brief introduction to RNA-seq and discusses quality control issues. Next, we will present the alignment step, quantification of expression and differential expression analysis. For downstream analysis we will focus on tools available through the Bioconductor project for manipulating and analysing bulk RNA-seq.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.