Course Materials for 2015

R Bio: Untangling Genomes

October, Montevideo, Uruguay

This course introduced students to untangling genomes through bioinformatics using R/Bioconductor and tools for pathway analysis. See the course web site for additional detail.

First Asia-Pacific Bioconductor Developer’s Meeting

September, Tokyo, Japan

Asia's first Bioconductor developer meeting.

BioC 2015: Where Software and Biology Connect

July, Seattle, Washington, USA

This conference highlights current developments within and beyond Bioconductor. Morning scientific talks and afternoon practicals provide conference participants with insights and tools required for the analysis and comprehension of high-throughput genomic data. 'Developer Day' preceeds the main conference on July 20, providing developers and would-be developers an opportunity to gain insights into project direction and software development best practices.

CSAMA2015

June, Brixen, Italy

The one-week intensive course Statistics and Computing in Genome Data Science teaches statistical and computational analysis of multi-omics studies in biology and biomedicine. It covers the underlying theory and state of the art (the morning lectures), and practical hands-on exercises based on the R / Bioconductor environment (the afternoon labs). The course covers the primary analysis ("preprocessing") of high-throughput sequencing based assays in functional genomics (transcriptomics, epigenetics, etc.) as well as integrative methods including efficiently operating with genomic intervals, statistical testing, linear models, machine learning, bioinformatic annotation and visualization. At the end of the course, you should be able to run analysis workflows on your own (multi-)omic data, adapt and combine different tools, and make informed and scientifically sound choices about analysis strategies. The course is intended for researchers who have basic familiarity with the experimental technologies and their applications in biology, and who are interested in making the step from a user of bioinformatics software towards adapting or developing their own analysis workflows. The four practical sessions of the course will require you to follow (and hopefully, modify) scripts in the computer language R.

Use R / Bioconductor for Sequence Analysis (Intermediate Course)

April, Seattle, USA

This INTERMEDIATE course is designed for individuals comfortable using R, and with some familiarity with Bioconductor. It consists of approximately equal parts lecture and practical sessions addressing use of Bioconductor software for analysis and comprehension of high-throughput sequence and related data. Specific topics include use of central Bioconductor classes (e.g., GRanges, SummarizedExperiment), RNASeq gene differential expression, ChIP-seq and methylation work flows, approaches to management and integrative analysis of diverse high-throughput data types, and strategies for working with large data. Participants are required to bring a laptop with wireless internet access and a modern version of the Chrome or Safari web browser.

Use R / Bioconductor for Sequence Analysis

February, San Francisco, USA

This course is directed at intermediate users wanting to make effective use of R and Bioconductor for the analysis and comprehension of high-throughput sequence data. The morning provides overall orientation to the packages and facilities available in Bioconductor, including and in-depth look at the central GenomicRanges infrastructure. The afternoon provides approaches to common challenges -- working with large data, placing statistical results in biological context, and effectively and reliably communicating results with other team members. The course combines lectures with extensive hands-on practicals; participants are required to bring a laptop with wireless internet access and a modern version of the Chrome or Safari web browser.

Learning R / Bioconductor for Sequence Analysis

February, San Francisco, USA

This course is directed at beginning and intermediate users who would like an introduction to the analysis and comprehension of high-throughput sequence data using R and Bioconductor. Day 1 focuses on learning essential background: an introduction to the R programming language; central concepts for effective use of Bioconductor software; and an overview of high-throughput sequence analysis work flows. The morning of Day 2 emphasizes use of Bioconductor for specific tasks, and in particular takes detailed look at RNA-seq differential expression work flow. The afternoon of Day 2 transitions to understanding effective approaches for managing larger challenges: strategies for working with large data, writing re-usable functions, developing reproducible reports and work flows, and visualizing results. The course combines lectures with extensive hands-on practicals; participants are required to bring a laptop with wireless internet access and a modern version of the Chrome or Safari web browser.

useR Course in Lyon, France

January, Lyon, France

BioC Europe 2015

January, EMBL, Heidelberg, Germany

TBA