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midterm project

This project explores BioConductor, an open-source software project designed to analyze and interpret genomic data. Initiated in 2001 by Robert Gentleman at Dana-Farber Cancer Institute, BioConductor provides essential tools for working with gene expression arrays, pathway graphs, and genomic sequence data. The project boasts contributions from approximately 25 core developers across institutions in the US and Europe. This report outlines the functionalities of BioConductor, offers usage examples using R, and illustrates how it aids in solving static problems on microarrays, highlighting its benefits for end-users and developers alike.

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midterm project

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  1. midterm project Course: Statistics in Bioinformatics Date:20070430 指導教授: 陳光琦 學生: 吳昱賢

  2. What is BioConductor? • What is BioConductor? • As the website saying • Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data.

  3. Outline • 軟體資訊 • 功能簡介 • 相關教學 • 使用心得

  4. Bioconductor • R software project for the analysis and comprehension of biomedical and genomic data. • Gene expression arrays (cDNA, Affymetrix) • Pathway graphs • Genome sequence data • Started in 2001 by Robert Gentleman, Dana Farber Cancer Institute. • About 25 core developers, at various institutions in the US and Europe. • Tools for integrating biological metadata from the web (annotation, literature) in the analysis of experimental metadata. • End-user and developer packages.

  5. Example R/BioC Packages

  6. wiki • most of the content on this wiki is aimed at developers of Bioconductor packages.

  7. Demo • Install R and Bioconductor packages.

  8. > MAplot(affybatch.example)

  9. 使用範例學習

  10. R console

  11. 結論 1.Bioconductor is a useful tool in dealing with static problem on microarray 2.affy example show the power of the R 3. I benefit a lots from this report like how to use bioC in R.

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