R/Bioconductor Workshop Session II - Bioconductor-ing
description
Transcript of R/Bioconductor Workshop Session II - Bioconductor-ing
R/Bioconductor WorkshopSession II - Bioconductor-ing
What is Bioconductor
Remember this guy??Fall 2001
Robert Gentleman, Program Head Computational
Biology FHCR
VJ Carey Wolfgang Huber
Rafael Irizarry
James W Macdonald
Herve Pages
Martin Morgan
Gordon Symth
A growing community
Citations Google Scholar(May 2008) reports 970 scientific documents
Screenshots
Mailing Lists (Bioc-help,Bioc-dev)Subject: Re: [BioC] analysis ChIP-seq dataSent By: [email protected] On:June 10, 2008 11:40 AM On Behalf Of:"Martin Morgan" <[email protected]>To:"Bogdan Tanasa" <[email protected]>Cc:[email protected]; bioconductor
Hi Bodan --
"Bogdan Tanasa" <[email protected]> writes:
> Hi everyone, > > I am in the process of analyzing a lot of ChIP-seq data and I am writing to ask > if an analysis module becomes available for R/Bioconductor anytime soon.
Visit the bioc-sig-sequencing news group (Cc'd in the reply)
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
Current packages include Biostrings (for lots of string matching / manipulation facilities) and ShortRead (for IO from ELAND or MAQ, for instance, plus additional sorting, counting, and qa-related functionality. There are posts in the bioc-sig-sequencing news group about package use.
Maybe others will reply (to bioc-sig-sequencing) with additional developments; I know people are working with and developing packages for this data in R.
Martin
goCluster
• goCluster is a tool for the analysis of expression data in conjunction with annotation data
• The package provides an object-oriented “framework” that allows to flexibly combine plugins to a specialized analysis method.
• goCluster provides modules for annotation data as well as clustering, statistical, and visualization methods.
goCluster Structure: 6 abstract classes define the general structure of the analysis task. Each abstract class can be filled with a specific module fullfilling the requested function in a special way.
goC
lust
er
clusterData
clusterAnnotation
clusterAlgorithm
clusterSignif
clusterStatistic
clusterVisual
Biological process
Example analysis: The plot shows a section of a hierarchical clustering that has been combined with gene ontology data using goCluster. The package has been able to automatically detect regions in the clustering that are enriched for specific GO-terms.
affylmGUI
GLAD: Gain and Loss Analysis of DNA
GLAD is devoted to the analysis of array CGH data (Comparative Genomic Hybridization)
✔ It allows the identification of breakpoints✔ It detects outliers✔ Each chromosomal regions are given a status (Gain, Normal or Loss)✔ Plot functions are available to draw genomic profiles
package required: AWS
Reference: Hupé et al., Bioinformatics (2004)
contact: [email protected] web site: http://bioinfo.curie.fr
Why I am falling in love with bioconductor Versatile and powerful– Room for development,
customized analysis, hundreds of software packages
Runs only Everything – Laptops, Servers, Windows, Linux, Unix, Ultrasparc
Support – Hundreds of bioinformaticians, biologists, Statisticians, IT dudes, mailing list, etc
Free!!!!
What are we waiting for?
Before we begin…