R/Bioconductor Workshop Session II - Bioconductor-ing

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R/Bioconductor WorkshopSession II -
Bioconductor-ing
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What is Bioconductor
Fall 2001
Remember this guy??
Gordon Symth
Herve Pages
Robert Gentleman, Program Head Computational
Biology FHCR
James W Macdonald
Rafael Irizarry
Martin Morgan
VJ Carey
Wolfgang Huber
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A growing community
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Citations

• Google Scholar(May 2008) reports 970 scientific
  documents

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Screenshots
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Mailing Lists (Bioc-help,Bioc-dev)
Subject Re BioC analysis ChIP-seq dataSent
By  bioconductor-bounces_at_stat.math.ethz.ch  OnJu
ne 10, 2008 1140 AM On Behalf Of"Martin Morgan"
ltmtmorgan_at_fhcrc.orggtTo"Bogdan Tanasa"
lttanasa_at_gmail.comgtCcbioc-sig-sequencing_at_r-project
.org bioconductor Hi Bodan -- "Bogdan Tanasa"
lttanasa_at_gmail.comgt writes gt Hi everyone, gt gt
I am in the process of analyzing a lot of
ChIP-seq data and I am writing to ask gt 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/bio
c-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
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goCluster
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.

• 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.

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.
Biological process
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affylmGUI
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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 glad_at_curie.fr web site
http//bioinfo.curie.fr
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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!!!!

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What are we waiting for?
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Before we begin