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Introduction to BioConductor

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。.

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Introduction to BioConductor

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  1. Introduction toBioConductor 　　　許家維　許文馨 　　　游崇善　陳彥如

  2. 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。

  3. Fred Hutchinson癌症研究中心

  4. 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.

  5. Main Features of the Bioconductor Project • Use of R. • Documentation and reproducible research. • Statistical and graphical methods. • Annotation. • Bioconductor short courses. • Open source.

  6. Bioconductor • 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.

  7. Installation of Bioconductor • 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("http://bioconductor.org/biocLite.R") • biocLite() # Installs the default set of Bioconductor packages. • 􀂆biocLite(c(“made4", “Heatplus"))# Command to install additional packages from BioC. • 􀂆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. • 􀂆getBioC()# Installs the getBioC.Rdefault set of BioConductorpackages.

  8. Release Packages􀂆

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

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

  11. 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

  12. 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

  13. Plot a Dendrogram

  14. 謝 謝 大 家

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