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Course Materials for 2014

New Package Hangout

December, Online!

This was a google hangout that took place online on December 10, 2014 in which Marc Carlson gave a short presentation on submitting a new package to Bioconductor, and then answered questions from commenters.

Learning R / Bioconductor for Sequence Analysis

October, Seattle, 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. Day 2 emphasizes use of Bioconductor for specific tasks: an RNA-seq differential expression work flow; exploratory, machine learning, and other statistical tasks; gene set enrichment; and annotation. Day 3 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; students are required to bring a laptop with wireless internet access and a modern version of the Chrome or Safari web browser.

Brazillian Cancer Epigenomics Workshop 2014

August, Rebeirão Preto, Brazil

Brazilian 2014 Cancer Epigenomics Workshop is an international forum of world renowned scientists in the area of cancer epigenomics and bioinformatics. In collaboration with the 60th Society of Brazilian Genetics Congress and the Latin American Bioconductor Foundation, we have put together a series of talks and hands-on training. The workshop will include high-level science talks plus a short course on bioinformatics using open source statistical tool - R and Bioconductor to analyze large-scale biological data. Bioconductor is a community driven platform, devoted to providing resources (via packages) for molecular biologist, computational biologist and bioinformatician interested in using R to analyze big bio-data, such as microarray and next-generation sequencing.

BioC 2014

July, Dana-Farber Cancer Institute, Boston, MA, 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. This year's conference is at the Dana-Farber Cancer Institute Longwood Campus, in Boston, MA. Visit the Conference Registration Page for more information.

Trends in genomic data analysis with R / Bioconductor

July, Boston, USA

The Bioconductor project is a leading development and analysis environment for bioinformatics, supported by a core of dedicated programmers and a broad contributing scientific community. The project is evolving rapidly along with sequencing technologies and the quantity of available genome annotation, and this workshop provides ISMB attendees with the inside track on the most recent and upcoming trends in Bioconductor. The workshop will begin with a high-level tour of leading Bioconductor packages and capabilities across a wide variety of disciplines, then will cover current advances for 1) accessing genomic annotation data such as ENCODE and the UCSC genome browser through the AnnotationHub architecture, 2) data and algorithm element designs for integrative analysis of large genomic data and annotation that permit scalable resource utilization at run-time, and 3) analysis of RNA-seq data. The workshop features the project leader Martin Morgan, co-founders and Core member Vince Carey, Advisory Board member Levi Waldron, and post-doctoral fellow Michael Love (Rafael Irizarry lab). This workshop is intended for a wide audience and will be valuable for beginner to experienced analysts of genomic data.

Introduction to Bioconductor for Sequence Analysis

June, useR! 2014, UCLA, USA,

DNA sequence analysis generates large volumes of data presenting challenging bioinformatic and statistical problems. This tutorial introduces Bioconductor packages and work flows for the analysis of sequence data. We learn about approaches for efficiently manipulating sequences and alignments, and introduce common work flows and the unique statistical challenges associated with 'RNAseq', variant annotation, and other experiments. The emphasis is on exploratory analysis, and the analysis of designed experiments.The workshop emphasizes orientation within the Bioconductor milieu; we will touch on the Biostrings, ShortRead, GenomicRanges, GenomicAlignments, DESeq2, and VariantAnnotation, and other packages, with short exercises to illustrate the functionality of each package.

Computational Statistics for Genome Biology (CSAMA)

June, Brixen-Bressanone, Italy

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.

Introduction to Bioconductor for High-Throughput Sequence Analysis

February, Seattle, USA

Introduction to Bioconductor for Sequence Analysis introduces users with some R experience to Bioconductor, especially working with high-throughput sequence data. Day 1 develops core R and Bioconductor concepts for working with large and complicated data. Participants will become familiar with data classes, packages, and scripting and programming concepts that are important for common and integrated work flows in Bioconductor. Day 2 will put these skills to use for the analysis of RNAseq differential expression data, including initial quality assessment, pre-processing, differential representation, annotation, and visualization. The course involves a combination of presentations and hands-on exercises; participants should come prepared with a modern laptop with wireless internet access.

Summer Bioinformatics Course, Ribeirao Preto, Brazil, January / February 2014

January, Ribeirao Preto, Sao Paulo, Brazil

R / Bioconductor material for portions of a course on the analysis and comprehension of high-throughput sequence data. Additional material available from the course web site and other course instructors.