BioC 2014

Dana-Farber Cancer Institute, Boston, MA, USA

2014-07-30 ~ 2014-08-01

Instructors

• TBA

Description

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.

Materials

Developer Day

Public Notes

Project Status

• pdf Introduction - Martin Morgan
• pdf Web site, videos, GenomeInfoDb - Sonali Arora
• html BiocCheck, html BioC AMI + StarCluster, html Subversion Server upgrade - Dan Tenenbaum
• pdf Shiny-phyloseq: Web Application for Interactive Microbiome Analysis with Provenance Tracking – Paul Joey McMurdie

Workshops

• html Debugging R Code.

Morning Talks

• pptx Mapping cellular hierarchy through single cell analysis – Guocheng Yuan
• pptx Analysis of somatic alterations in the cancer genome – Matthew Meyerson
• pdf Software for Enabling Genomic Data Analysis – Michael Lawrence
• pdf Analysis of small molecule molecular data in R – Kevin Horan
• pdf Flexible analysis of RNA-seq data with Ballgown, Alyssa Frazee
• presentation Epiviz(r): turning a genome browser into an interactive display device – Hector Corrada Bravo

Afternoon Labs

Thursday 1:00 - 2:50

• pdf (slides), pdf R (lab) R / Bioconductor for everyone – Martin Morgan
• html | Rmd | R Practical and html | Rmd | R Tutorial, Introduction to Flow Cytometry Data Analysis using OpenCyto and BioConductor – Greg Finak
• pdf | Rnw | R | data file Analysis of 450k methylation data with the minfi package – Kasper Hansen

• pdf
  R	Data file

• pdf Visualisation and assessment of ChIP-seq quality using ChIPQC and Diffbind packages – Tom Carroll

Thursday 3:10 - 5:00

• pdf Learn how to use Bioconductor to perform common tasks on your high-throughput sequencing data – Hervé Pagès
• pdf | html | md Differential gene- and exon-level expression analyses for RNA-seq data using edgeR, voom and featureCounts – Mark Robinson
• html | Rmd | R Genetics of gene expression: computation and integrative prediction – Vincent Carey
• html | Rmd | R R / Bioconductor packages for Proteomics – Laurent Gatto

• Rpres

  R Meta-analysis of genomics experiments using Bioconductor – Levi Waldron

Friday 1:00 - 2:50

• pdf | Rnw | R Analysis of RNA-Seq using the DESeq2 package – Michael Love. Data files: Homo_sapiens.GRCh37.75.subset.gtf.gz sampleTable.csv
• pdf | html | Rmd | R CRISPRseek: Design of target-specific guide RNAs in CRISPR-Cas9 genome-editing systems – Julie Zhu

• html

  Rmd

  R

  PDF - background

  zip - references

  zip - figures Integrated pathway analysis of multiple ‘omics datasets Aedin Culhane

• Annotation Workflow

  AnnotationHub vignette Bioconductor annotations: using and sharing resources – Marc Carlson

Friday 3:10 - 5:00

• pdf | R | R - Solutions Parallel Computing with Bioconductor in the Amazon Cloud – Valerie Obenchain
• pdf | R | pkg Variant calling with Bioconductor – Michael Lawrence
• pdf Visualisation and assessment of ChIP-seq quality using ChIPQC and Diffbind packages – Tom Carroll