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- BioC 2010
BioC 2010
Seattle, WA
2010-07-29 ~ 2010-07-30
Instructors
- David Fredricks
- Stephen Friend
- Jay Shendure
- Atul Butte
- Simon Tavare
- Paul Flicek
- Lior Pachter
- Simon Anders
- Patrick Aboyoun
- Vincent Carey
- Marc Carlson
- Steffen Durinck
- Greg Finak
- Nishant Gopalakrishnan
- Wolfgang Huber
- Michael Lawrence
- James MacDonald
- Davis McCarthy
- Martin Morgan
- Herve Pages
- Mark Robinson
- Chao-Jen Wong
- Julie Zhu
Description
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
Morning Talks
- The Human Microbiome - David Fredricks, Fred Hutchinson Cancer Research Center.
- Better Maps of Disease: Building a commons for evolving generative models of disease - Stephen Friend, SAGE Bionetworks.
- Next Generation Mendelian Genetics by Exome Sequencing - Jay Shendure, University of Washington.
- Exploring Genomic Medicine Through Integrative Bioinformatics - Atul Butte, Stanford Center for Biomedical Informatics Research.
- Sparse partitioning: a tool for analyzing regression problems with many tertiary predictors - Simon Tavare, University of Southern California.
- Generation gap: How existing bioinformatics resources are adapting to high-throughput sequencing - Paul Flicek, European Bioinformatics Institute.
- Statistical Challenges in transcriptome sequencing - Lior Pachter, University of California, Berkeley.
- Differential expression analysis for sequencing count data - Simon Anders, European Bioinformatics Institute.
Afternoon Labs
Introduction to R
Instructor: Chao-Jen Wong
Install command:
source("http://bioconductor.org/course-packages/install-HTSTrack.R")
Efficient R Programming
Instructor: Martin Morgan
Install command:
source("http://bioconductor.org/course-packages/install-EfficientR.R")
Using limma for differential expression
Instructor: James W. MacDonald
Data mining with biomaRt
Instructor: Steffen Durinck
ChIPpeakAnno Practical
Instructor: Lihua Julie Zhu
Transcript centric annotations and high-throughput sequencing
Instructors: Marc Carlson / Herve Pages
Install command:
source("http://bioconductor.org/course-packages/install-HTSTrack.R")
Bioconductor tools for input and quality assessment of high-throughput sequence data
Instructors: Patrick Aboyoun / Martin Morgan
- Four exercises using Bioconductor Sequence Infrastructure
- Exercises: Reading and Manipulating Short Reads
- Exercises: An Introduction to Rsamtools
- Exercises: A Simple ChIP-Seq Workflow
- Exercises: A Simple RNA-seq Use Case
Install command:
source("http://bioconductor.org/course-packages/install-HTSTrack.R")
Analyzing and Visualizing ChIP-seq Data
Instructor: Michael Lawrence
Analysis of genome-scale count data in Bioconductor
Instructors: Mark Robinson / Davis McCarthy
Using image data for statistical analysis and modeling
Instructor: Wolfgang Huber
- Using image data for statistical analysis and modeling (slides)
- Using image data for statistical analysis and modeling (R script)
- Image of actin in cells
- Image of DNA in cells
- Image of tubulin in cells
Genetics of gene expression: comprehensive eQTL search
Instructor: Vince Carey
Gene centric annotations
Instructor: Marc Carlson
Install command:
source("http://bioconductor.org/course-packages/install-HTSTrack.R")
Analyzing flow cytometry data in Bioconductor
Instructors: Nishant Gopalakrishnan / Chao-Jen Wong
- Brief Intro to R for Flow Packages Users
- Analyzing flow cytometry data in Bioconductor
- Flow cytometry analysis Lab
- Flow cytometry analysis Lab Solutions
Install command:
source("http://bioconductor.org/course-packages/install-flowTrack.R")
Automated Gating and Metaclustering of High Content Flow Cytometry Data
Instructor: Greg Finak
- Automated Gating and Metaclustering for Flow Cytometry Data
- Automated Gating and Metaclustering for Flow Cytometry Data (white paper)
Install command:
source("http://bioconductor.org/course-packages/install-flowTrack.R")