Course Google-doc

Last-minute instructions are available on the course google doc, active before and during the course.

To start using an AMI, visit https://courses.bioconductor.org/ .

Abstract

DNA sequence analysis generates large volumes of data that present challenging bioinformatic and statistical problems. This tutorial introduces established and new Bioconductor packages and workflows for analyzing sequence data. The Bioconductor project (http://bioconductor.org) is a widely used collection of nearly 1000 R packages for high-throughput genomic analysis. Approaches for efficiently manipulating sequences and alignments and other common work flows will be covered along with 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 will touch on the Biostrings, ShortRead, GenomicRanges, DESeq2, VariantAnnotation, and other packages, with short exercises to illustrate the functionality of each package.

Goals

1. Gain overall familiarity with Bioconductor packages for high-throughput sequence analysis, including Bioconductor vignettes and classes.

2. Obtain experience running bioinformatic workflows for data quality assessment, RNA-seq differential expression, and manipulating variant call format files.

3. Appreciate the importance of ranges and range-based manipulation for modern genomic analysis

4. Learn 'best practices' for working with large data

Outline (tentative!)

Time | Topic ----------------- | ---------------------------------------------------------------------------- 10:00am - 10:15am | Welcome & Overview (Course Overview & AMI set-up) 10:20am - 11:00am | Introduction: Analysis and Comprehension of High Throughput Genomic Data 11:05am - 12:00pm | Sequences, Alignments, and Large Data 12:00pm - 1:00pm | Lunch, Divercity (15 mins walk from AIST) 1:00pm - 2:00pm | RNA-Seq Known-gene Differential Expression 2:05pm - 3:00pm | Gene, Genome, and Variant Annotation 3:00pm - 3:30pm | Coffee break, Espresso Americano (Telecom Center, 5 mins walk from AIST) 3:30pm - 4:00pm | Topic ??? / Bring your own data 4:05pm - 4:15pm | Feedback

Prerequisites

The workshop assumes an intermediate level of familiarity with R, and basic understanding of biological and technological aspects of high-throughput sequence analysis. Participants should come prepared with a modern wireless-enabled laptop and web browser installed.

Installation

Follow these steps:

• Install R version 3.2.2 from https://cran.r-studio.com

• Install the Bioconductor installer

  source("https://bioconductor.org/biocLite.R")
  

• Install the course package and depedencies

  biocLite("devtools")
  biocLite("Bioconductor/BiocAsiaPacific2015", dependencies=TRUE)
  

Intended Audience:

This workshop is for professional bioinformaticians and statisticians intending to use R/Bioconductor for analysis and comprehension of high-throughput sequence data.

Reference

Huber et al. (2015) Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods. Jan 29;12(2):115-21.