Transcript 07.12.17_Intro to BioConductor

Introduction to
BioConductor
許家維
游崇善
許文馨
陳彥如
Bioconductor
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BioConductor起初是由Fred Hutchinson癌症研究
中心發起的計畫，之後有許多來自不同國家的研
究人員參與，這個計畫是一個為了分析理解基因
體資料的開放源碼計劃。
這個計畫以R統計程式語言為基礎，搭配R統計語
言可以進行許多的基因體資料分析，每年會推出
兩個更新版本，或是搭配著R統計語言版本更新，
大部分的BioConductor的套件是用來分析各種不
同基因微陣列資料的。
Fred Hutchinson癌症研究中心
Goals of the Bioconductor Project
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Provide access to a wide range of powerful statistical
and graphical methods for the analysis of genomic data.
Facilitate the integration of biological metadata in the
analysis of experimental data: e.g. literature data from
PubMed, annotation data from LocusLink.
Allow the rapid development of extensible, scalable, and
interoperable software.
Promote high-quality documentation and reproducible
research.
Provide training in computational and statistical methods
for the analysis of genomic data.
Main Features of the Bioconductor
Project
Use of R.
 Documentation and reproducible
research.
 Statistical and graphical methods.
 Annotation.
 Bioconductor short courses.
 Open source.
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Bioconductor
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Bioconductor
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Bioconductoris an open source and open development
software project for the analysis of bioinformaticand genomic
data.
The project was started in the Fall of 2001 and includes 24
core developers in the US, Europe, and Australia.
Bioconductorwww.bioconductor.org
- software, data, and documentation (vignettes);
- training materials from short courses;
- mailing list.
Installation of Bioconductor
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Installation of Bioconductor
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The latest instructions for installing Bioconductorpackages are available on the
Download page.
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To install BioConductorpackages, execute from the R console the following
commands:
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source("http://bioconductor.org/biocLite.R")
biocLite() # Installs the default set of Bioconductor packages.
biocLite(c(“made4", “Heatplus"))# Command to install additional packages
from BioC.
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source("http://www.bioconductor.org/getBioC.R")# Sources the
getBioC.Rinstallation script, which works the same way as biocLite.R, but
includes a larger list of default packages.
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getBioC()# Installs the getBioC.Rdefault set of BioConductorpackages.
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Release Packages
Bioconductor Software Packages
Software packages are sub divided into
seven categories.
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Each contains a long list of contributed
packages.
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Bioconductor Annotation Data
Packages
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There are over 1,800 bioconductor
annotation packages. These packages
provide annotation on the genes on
microarrays.
Annotations of AffymetrixGeneChip
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Affymetrix 為全球生物晶片產業之主要領
導廠商,1993 年成立於美國加州
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Some useful packages for Genomic Data
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Gene Ontology (GO) analysis: GOstats;
goCluster
 Chromosome maps: geneplotter
 PhylogeneticAnalysis: ape
 Protein Structure Analysis: Bio3D
 Motif identification in promoter regions:
COSMO
Plot a Dendrogram
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