Developer Day
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