Introduction to BioConductor 許家維 許文馨 游崇善 陳彥如

Bioconductor 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 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.

Bioconductor  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  The latest instructions for installing Bioconductorpackages are available on the Download page.  To install BioConductorpackages, execute from the R console the following commands: source(" biocLite() # Installs the default set of Bioconductor packages.  biocLite(c(“made4", “Heatplus"))# Command to install additional packages from BioC.  source(" Sources the getBioC.Rinstallation script, which works the same way as biocLite.R, but includes a larger list of default packages.  getBioC()# Installs the getBioC.Rdefault set of BioConductorpackages.

Release Packages

Bioconductor Software Packages Software packages are sub divided into seven categories. Each contains a long list of contributed packages.

Bioconductor Annotation Data Packages There are over 1,800 bioconductor annotation packages. These packages provide annotation on the genes on microarrays.

Annotations of AffymetrixGeneChip 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

Some useful packages for Genomic Data  Gene Ontology (GO) analysis: GOstats; goCluster  Chromosome maps: geneplotter  PhylogeneticAnalysis: ape  Protein Structure Analysis: Bio3D  Motif identification in promoter regions: COSMO

Plot a Dendrogram

謝 謝 大 家