BioC2013

Seattle, USA

2013-07-17 ~ 2013-07-19

Instructors

• TBA

Description

Developer Day is July 17, 2013. Conference is July 18-19, 2013. This conference highlights current developments within and beyond Bioconductor, an international open source and open development software project for the analysis and comprehension of high-throughput genomic data.

Materials

Developer Day

Schedule

Introduction - Martin Morgan

rhdf5-supported variant calling - Paul Pyl

Quick Fix Debugging, Debugging (solved)

BatchJobs demo - Michael Lawrence

BaseSpaceR - Adrian Alexa

RStudio and Shiny - Joe Cheng

Tackling Big Data with R - Simon Urbanek

knitr / Yihui Xie

slides | R Markdown

Debugging in R and C

profiling.md, line-profiling.R

Debugging in R: Presentation | R Code

c-debugging.md, c-crash.R, c-valgrind.R, c-valgrind.c

Morning Talks

Big Science on a Small Budget / Tim Triche

A computational Bayesian approach to gene regulatory network estimation / Matthew McCall

Dissection of xenograft tumor and stromal response to VEGF inhibition from RNA-Seq data / Gregoire Pau PDF Keynote

Computational anaylses of high-throughput spatial proteomics data / Laurent Gatto

Associating differential ER binding with clinical outcome in breast cancer / Rory Stark

Detection and characterization of complex rearrangements in tumor genomes / Aaron Quinlan

Afternoon Labs

Cheminformatics of Drug-like Small Molecules / Thomas Girke

Slides | R Code

Differential analysis of ChIP-seq data / Rory Stark

PDF | Data Files

minfi and shinyMethyl: a winning pair of R-packages for the analysis of methylation data / Jean-Philippe Fortin

Slides

R Code

ReportingTools / Jessica Larson

Presentation | Code

DESeq2/DEXSeq / Alejandro Reyes, Wolfgang Huber

R Code | Rnw Code | PDF

Presentation: PDF

key

Reproducible Research with RStudio, knitr, and git / Jeffrey Johnston

Tarball | PDF

RGalaxy/AnnotationHubServer / Dan Tenenbaum

RGalaxy Lab vignette | AnnotationHubServer presentation

Variant Calling with R/Bioconductor / Michael Lawrence

Slides | R code

Annotations in Bioconductor / Marc Carlson, Valerie Obenchain

Annotation Resources | Annotating Genomic Ranges

Shiny: Interactive web-based interfaces in R / Joe Cheng, Jeff Allen, Shawn Balcome

Presentation

Efficient manipulation of high-throughput sequencing data in Bioconductor / Hervé Pagès

Slides

From reads to genes in less than 10 R commands / Wei Shi

PDF | R Code

A Bioconductor pipeline for the analysis of ChIP-Seq experiments / Xuekui Zhang, Sangsoon Woo, Arnaud Droit, Renan Sauteraud

PDF

R/Bioconductor for Everyone / Martin Morgan

Slides | R Code

Lab Slides | Lab R Code