Training Courses
As part of its work with the Babraham Institute, the Bioinformatics group runs a regular series of training courses on many aspects of bioinformatics.
All of our training is now mananged via the BioTrain.TV website and you should visit there to look at the course dates we have available and the course topics which we routinely run.
Where possible we also aim to make the material from our courses publicly available so that anyone who wants to can download them for their own use. Course material is still distributed from this site and can be seen below.
This material is distributed under a Creative Commons Non-Commerical license, which means you are free to download and reuse the content as long as you say that it came from us, and you're not using it for directly commercial purposes (ie charging people to come to a course based off our material).
Core Bioinformatics Skills
- R (tidyverse) Courses
- R (just core) Courses
- Other R courses
- Python Courses
- Perl Courses
- Unix Courses
- Machine learning
Statistics
- Modular Statistics courses using R
- Statistical Analysis using R
- Modular statistics courses using GraphPad Prism
- Data Resources
- Next Generation Sequencing
- Quality control in Sequencing Experiments
- Analysing Mapped Sequence Data with SeqMonk
- RNA-Seq Analysis
- 10X Single Cell RNA-Seq Analysis
- ChIP-Seq Analysis
- Analysing bisulfite methylation sequence data
- Proteomics
- Modelling
- Interpretation and Presentation
- Course Manual (pdf)
- Course Manual (doc)
- Course Exercises (pdf)
- Course Exercises (doc)
- Code used in the course (zip)
- Course Slides (pptx)
- Course Slides (pdf)
- Course Exercises (docx)
- Course Exercises (pdf)
- Course Data (zip)[2.2MB]
- Course Manual (pdf)
- Course Manual (docx)
- Course Slides (pdf)
- Course Slides (pptx)
- Course Exercises (pdf)
- Course Exercises (docx)
- Course Data (zip)
- Course Manual (docx)
- Course Manual (pdf)
- Course Slides (pdf)
- Course Slides (pptx)
- Course Exercises (pdf)
- Course Exercises (docx)
- Course Data (zip)
- Intro to R with Tidyverse Slides (pdf)
- Intro to R with Tidyverse Slides (pptx)
- Course Exercises (pdf)
- Course Exercises (doc)
- Answers to exercise questions (html)
- Course data (zip)
- Course Manual (pdf)
- Course Manual (docx)
- Course Exercises (pdf)
- Course Exercises (doc)
- Intro to R Slides (pdf)
- Intro to R Slides (pptx)
- R command cheatsheet (pdf)
- Answers to exercise questions (html)
- Course data (zip)
- Course Manual (pdf)
- Course Manual (docx)
- Course Exercises (pdf)
- Course Exercises (docx)
- Course data (zip)
- Course Manual (pdf)
- Course Manual (docx)
- Course Exercises (pdf)
- Course Exercises (docx)
- Presentation Slides (pdf)
- Presentation Slides (pptx)
- Course data (zip)
- Exercise Answers (html)
- Course Slides (pptx)
- Course Slides (pdf)
- Course Exercises (docx)
- Course Exercises (pdf)
- Course Data (zip)
- Exercise Answers (html)
- Course Slides (pdf)
- Course Slides (pptx)
- Course Exercises (docx)
- Course Exercises (pdf)
- Course data (zip)
- Exercise Answers (html)
- Initial setup instructions (html)
- Exercises (html)
- Course Slides (pdf)
- Course Slides (pptx)
- Course Data (zip)
- Course Slides (pdf)
- Course Slides (pptx)
- Course Exercises (pdf)
- Course Exercises (docx)
- Unix cheat sheet (pdf) (External content from Fosswire)
- Course Data (tar.gz) [5MB]
- Course Slides (pdf)
- Course Slides (pptx)
- Course Exercises (pdf)
- Course Exercises (docx)
- Course Data (zip)
- BS-Seq data processing lecture (pptx)
- BS-Seq data processing lecture (pdf)
- BS-Seq data processing exercises (docx)
- BS-Seq data processing exercises (pdf)
- Visualisation and exploration lecture (pptx)
- Visualisation and exploration lecture (pdf)
- SeqMonk tools for methylation analysis (pptx)
- SeqMonk tools for methylation analysis (pdf)
- Visualisation and exploration practical (docx)
- Visualisation and exploration practical (pdf)
- Differential methylation lecture (pptx)
- Differential methylation lecture (pdf)
- Differential methylation practical (docx)
- Differential methylation practical (pdf)
- Data for all practicals (tar) [WARNING 9GB]
- Course VirtualBox Machine Image (ova) [WARNING 9GB]
- Gene Lists Course Slides (pptx)
- Gene Lists Course Slides (pdf)
- Gene Set analysis practical (docx)
- Gene Set analysis practical (pdf)
- Gene Set Analysis in R Practical (docx)
- Gene Set Analysis in R Practical (pdf)
- Gene List and Motif Practical Data (zip) [1 MB]
- ChIP-Seq Course Slides (pptx)
- ChIP-Seq Course Slides (pdf)
- Processing ChIP data exercise (docx)
- Processing ChIP data exercise (pdf)
- Exploring ChIP data exercise (docx)
- Exploring ChIP data exercise (pdf)
- Analysing ChIP data exercise (docx)
- Analysing ChIP data exercise (pdf)
- Course Linux Mapping Data (tar.gz) (660MB)
- Course Desktop Analysis Data (zip) (1.6GB)
- Course Presentation (pptx)
- Course Presentation (pdf)
- Practical instructions (docx)
- Practical instructions (pdf)
- Multi-Condition Exercise (docx)
- Multi-Condition Exercise (pdf)
- Yeast data for mapping (tar.gz) (470MB)
- Mapped mouse data for seqmonk (zip) (2.4GB)
- Introduction to 10X preparation and processing (pptx)
- Introduction to 10X preparation and processing (pdf)
- Course Slides (pptx)
- Course Slides (pdf)
- Course Excercises (docx)
- Course Excercises (pdf)
- Course Data (tar.gz) [405MB]
- Introduction to Modelling (pdf)
- Introduction to Chemical Kinetics (pdf)
- COPASI Modelling Tutorial (pdf)
- Course Data (zip) [9.3MB]
- Introduction to Proteomics Slides (pdf)
- Introduction to Proteomics Slides (pptx)
- Proteomics Exercises (pdf)
- Proteomics Exercises (docx)
- MSstats exercise answer
- Proteomics Course Data (zip)
Application focussed courses
Analysing Mapped Sequence Data with SeqMonk (Half day)
Course Material:
Statistical Analysis using R
Course Material:
Statistical Analysis using GraphPad Prism (Two days)
Course Material:
Learning to Program with Perl (6 x 1.5 hour sessions)
Course Material:
Introduction to Python
Course Material:
Advanced Python
Course Material:
Understanding Object Oriented Python
Course Material:
Introduction to R with Tidyverse
Course Material:
Post-Course Material:
Introduction to Core R
Course Material:
Advanced Core R
Course Material:
Plotting complex figures with Core R
Course Material:
Advanced R with Tidyverse
Course Material:
Using R Notebooks
Course Material:
Plotting figures with ggplot
Course Material:
Writing R Packages
Course Material:
Introduction to Shiny
Course Material:
Using git and GitHub with RStudio
Course Material:
An Introduction to Linux
Course Material:
An Introduction to Machine Learning
Course Material
Analysing bisulfite methylation sequencing data
Course Material:
Extracting biological information from gene lists
Course Material:
ChIP-Seq Analysis
Course Material:
RNA-Seq Analysis
Course Material:
Single Cell RNA-Seq Analysis
Course Material:
An Introduction to Biological Big Data
Course Material:
Quality Control in Sequencing Experiments
Course Material:
An Introduction to Mathematical Modelling
Course Material:
An Introduction to Proteomics
Course Material:
Scientific Figure Design
Course Material:
Research Integrity: How To Be A Good Scientist
Course Material:
An Introduction to Using OneNote as a Laboratory Notebook
Course Material:
- OneNote Slides (pptx)
- OneNote Slides (pdf)
- OneNote manual (docx)
- OneNote manual (pdf)
- OneNote exercises (docx)
- OneNote exercises (pdf)
- OneNote Course Data files (zip)