About the Course
This one-week intensive course teaches current approaches in the statistical and computational analysis of large-scale experiments in biology. The course focuses on the methods for downstream analyses of high-throughput sequencing experiments including RNA sequencing (differential expression), DNA sequencing (variant calling), ChIP-Seq. Lectures also cover essentials including statistical testing, linear models, machine learning, visualisation and bioinformatic annotation.
Emphasis is given to practical problem solving skills using open-source software from the Bioconductor, CRAN and other projects. The course is intended for researchers who have basic familiarity with the experimental technologies and the biology of the genome, and who are interested in developing their own, advanced data analyses using a scripting environment. The four practical sessions of the course will require simple script understanding in the computer language R. A tutorial on the required more advanced features of R will be provided, students are advised to familiarize themselves with the very basics of R beforehand. (Consider one of the many online resources or books, e.g. R-Intro from the R Project, Germán Rodríguez, R-Studio.
Please consult material from the 2013 course to get an impression of the scope and level of the teaching.
- Introduction to R and Bioconductor
- Elements of statistics: hypothesis testing, multiple testing, regression, regularisation, clustering and classification (machine learning), visualisation
- Computing with sequences and genomic intervals
- RNA-Seq data analysis and differential expression
- DNA Variant calling
- Working with annotation - genes, genomic features and variants
Course StructureThe course consists of
- morning lectures: 20 x 45 minutes: Monday to Friday 8:30am - 12:00am
- 4 practical computer tutorials in the afternoons (2pm - 5pm) on Monday, Tuesday, Thursday and Friday
The course material will be provided in electronic form during the course. To prepare, you might consult material from the 2013 course, material from other related courses in 2013 and 2014, the general Bioconductor documentation and specific package vignettes.
The labs will be worked on in groups with expert guidance (all lecturers from the morning sessions plus teaching assistants).
Participants are required to bring their own laptops with the most recent release versions of R and Bioconductor installed. A WiFi network card is welcome to connect to our local network, however, no connections to the internet will be possible from the WLAN at the course venue.
We meet in front of Palazzo Vescovile at 1:50 pm. We need to split into 3 groups (A, B, C)
Group A: guided tour in English starts at 2:00
Group B: guided tour in German starts at 2:15
Group C: guided tour in English starts at 3:00
Between 2pm and 3pm, participants of group C can take a free visit at other expositions in Palazzo Vescovile. Same option for groups A&B, from 3:00 to 4:00.
At 4:15pm we take the bus in front of the Office of Tourism (just behind Palazzo Vescovile), Viale Ratisbona 9 http://www.brixen.org. Bus will bring us to the Plose Ropeway. We will have a walk from the arrival of the ropeway to RossAlm.
We will have dinner at RossAlm (around 7pm) and then walk back (at 8:30 at most) to the bus waiting (but not forever) for us. Bus will leave from the parking lot at 9:30pm.
No Internet Access
Please note: the course venue will not be able to provide you with internet access. You will be able to connect to a local network that provides the course material.