1 / 17

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。.

jacob
Download Presentation

Introduction to BioConductor

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related