Summer school course materials collection

CRUK Bioinformatics Summer School 2018: Functional Genomics

23rd - 27th July 2018: Craik-Marshall Room, Downing Site, University of Cambridge


Functional genomics looks at the dynamic aspects of how the genome functions within cells, particularly in the form of gene expression (transcription) and gene regulation. This workshop surveys current methods for functional genomics using high-throughput technologies.

High-throughput technologies such as next generation sequencing (NGS) can routinely produce massive amounts of data. However, such datasets pose new challenges in the way the data have to be analyzed, annotated and interpreted which are not trivial and are daunting to the wet-lab biologist. This course covers state-of-the-art and best-practice tools for bulk RNA-seq and ChIP-seq data analysis, and will also introduce approaches for analysing data arising from single-cell RNA-seq studies.


Enthusiastic and motivated wet-lab biologists who want to gain more of an understanding of NGS data and eventually progress to analysing their own data


The course will include a great deal of hands-on work in R and at the command line. In order for you to make the most of the course we strongly recommend that you take an introductory course, or have sufficient experience in the following areas:

More specific requirements and references can be found here

Data files for course are here. There is a zip-file for each course and a sizes.txt file with zip sizes (Warning: Single-cell one is BIG!)



During this course you will learn about:-


After the course you should be able to:-

Day 0 (July 22nd )

**SOCIAL 18:00 - .. Informal get-together at The Grain and Hop Store (close to accommodation in Downing College) Join us for a drink and dinner (self-paying), and to meet your colleagues for the next few days

**Note that the Training Room in Craik-Marshall building (1st Floor) will be open from 9am. School etherpad (E-whiteboard) is here **

Day 1 (July 23rd)

Day 2 (July 24th)

Please note we use several Rstudio Notebook html files as material for the RNAseq course. To obtain the source code (.Rmd file) you can simply click on the code button in the top right-hand corner).

Day 3 (July 25th)

NB We do not have sufficient time to teach this entire course in half a day. However, some concepts are covered in the Bulk RNASeq course and we provide the link to the full materials. Please note, that on occasions where all of the material was used, it resulted in a five-day course(!). We will teach topics that should be of interest even to those not interested in single-cell work.

SOCIAL: Punting trip - leave from Mill Lane punting site at 18:00 (~10 min walk from Craik-Marshall) Google Map. Scudamore’s Web-site & Mill lane map.

Day 4 (July 26th)

**SOCIAL: Summer School evening meal & Reception at the nearby Downing College at 18:00 to 22:30.. If you do not wish to attend this meal (free to attendees) then please let us know ASAP. Smart casual dress. Downing College, Regent Street, Cambridge, CB2 1DQ (Site map in link below)
Drinks Reception 18:00- 19:45 West Lodge
Dinner 19:45 -22:30 Grace Howard Room

Day 5 (July 27th)