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Mon 1 Jul - Fri 5 Jul 2019
09:30, ...

Venue: Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Provided by: Bioinformatics


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Summer School - Bioinformatics for Biologists: An introduction to Data Exploration, Statistics and Reproducibility
Special£

Mon 1 Jul - Fri 5 Jul 2019

Description

This 1-week course aims to provide an introduction to the best practices and tools needed to perform bioinformatics research effectively and reproducibly.

Focusing on solutions around handling biological data, we will cover introductory lessons in data manipulation and visualisation in R, statistical analyses, and reproducibility. The R component of the course will cover from basic steps in R to how to use some of the most popular R packages (dplyr and ggplot2) for data manipulation and visualisation. No prior R experience or previous knowledge of programming/coding is required. The course also includes introductory sessions in statistics and working examples on how to analyse biological data. At the end of the course we will address issues relating to reusability and reproducibility.

More information about the course can be found here.

This course is run in collaboration with the Institute of Continuing Education.

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.

Target audience
  • This course is aimed at individuals working across biological and biomedical sciences who have little to no experience in bioinformatics.
  • The course is open to Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
  • Please note that all participants attending this course will be charged a registration fee.
  • Non-members of the University of Cambridge to pay £575
  • All Members of the University of Cambridge to pay £250

A booking will only be approved and confirmed once the fee has been paid in full.

  • Further details regarding eligibility criteria are available here
Prerequisites
  • Biological/Biomedical background knowledge
  • No previous knowledge of programming/coding is required for this course.
Sessions

Number of sessions: 5

# Date Time Venue Trainers
1 Mon 1 Jul   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Matthew Eldridge,  Dr Sandra Cortijo,  Hugo Tavares,  Katharina Lauer
2 Tue 2 Jul   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Dr Sandra Cortijo,  Hugo Tavares
3 Wed 3 Jul   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Dr Matt Castle
4 Thu 4 Jul   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Hugo Tavares,  Dr Sandra Cortijo,  Martin van Rongen
5 Fri 5 Jul   09:30 - 17:15 09:30 - 17:15 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Dr Stephen J. Eglen,  Ashley Sawle,  Mark Fernandes,  Kim Gurwitz
Topics covered

Bioinformatics, Data visualisation, Data handling

Objectives

As a result of attending the course, participants should be able to:

  • Define opportunities and challenges of using bioinformatics in research
  • Format and clean, visualise, and explore datasets in R
  • Evaluate which statistical tests are appropriate for a dataset
  • Implement reproducible and reusable methods for their research
Aims

The aim of this course is to:

  • Encourage the development of the bioinformatics skills needed to process biological data effectively
  • Provide practical experience with, and guidance on, how to manage and analyse examples of biological data
  • Introduce best practices with regards to working with data reproducibly
Format

Presentations, demonstrations, and practicals

Timetable

Day 1 Getting you set up for Bioinformatics analyses
9:30 - 9:45 Welcome
9:45 - 10:45 Bioinformatics opportunities and challenges in handling biological data
10:45 - 11:00 Tea/ Coffee break
11:00 - 13:00 Data organisation in spreadsheets
13:00 - 14:00 Lunch (provided)
14:00 - 15:30 Introducing R
15:30 - 15:45 Tea/ Coffee break
15:45 - 17:30 Data structures
Day 2 Data Manipulation and Visualisation in R
9:30 - 9:50 R recap
9:50 - 10:45 Data manipulation in R
10:45 - 11:00 Tea/ Coffee break
11:00 - 13:00 Data visualisation in R
13:00 - 14:00 Lunch (provided)
14:00 - 15:30 Data manipulation and visualisation in R (cont.)
15:30 - 15:45 Tea/ Coffee break
15:45 - 17:30 Data manipulation and visualisation in R (cont.)
Day 3 Introduction to Statistics for Data Analysis
9:30 - 10:30 Simple hypothesis testing
10:30 - 10:45 Tea/ Coffee break
10:45 - 13:00 Simple hypothesis testing (cont.)
13:00 - 14:00 Lunch (provided)
14:00 - 15:30 Introduction to programming
15:30 - 15:45 Tea/ Coffee break
15:45 - 17:30 Statistics for big data
Day 4 Introduction to Exploratory Analysis of RNA-seq data in R
9:30 - 10:30 Introduction
10:30 - 10:45 Tea/ Coffee break
10:45 - 13:00 RNA-seq exploratory analysis
13:00 - 14:00 Lunch (provided)
14:00 - 15:30 RNA-seq exploratory analysis (cont.)
15:30 - 15:45 Tea/ Coffee break
15:45 - 17:30 RNA-seq exploratory analysis - advanced topics
Day 5 Introduction to Reproducibility and Reusability
9:30 - 9:45 Introduction to reproducibility and reusability
9:45 - 10:45 Data organisation
10:45 - 11:00 Tea/ Coffee break
11:00 - 12:30 Reproducible and reusable reports with Rmarkdown
12:30 - 13:30 Lunch (provided)
13:30 - 15:00 Introduction to version control with Git in R
15:00 - 15:15 Tea/ Coffee break
15:15 - 16:15 Introduction to sharing code with GitHub
16:15 - 17:15 Wrap up and next steps
Registration fees
  • All participants attending this course will be charged a registration fee.
  • Non-members of the University of Cambridge to pay 575.00 GBP
  • All Members of the University of Cambridge to pay 250.00 GBP.
  • A booking will only be approved and confirmed once the fee has been paid in full.
  • Further details regarding the charging policy are available here
Duration

5

Theme
Specialized Training

Booking / availability