12、国外大学研究所收集谷歌ppt谷歌-ngs-pipeline的ppt slides2.pptVIP

* * * * * * * * * * * * * * * * * * * * * * * * * * * * * Overview of Bioconductor Aedín Culhane aedin@ /~aedin /research/aedin-culhane Bioconductor Biannual release (normally April, October) to coincide with R release. Current: Bioconductor 2.9 (release coincide with R 2.14) To install use script on Bioconductor Website source(/biocLite.R) biocLite() Packages Overview BioConductor web site Bioconductor BiocViews Task view Software Annotation Data Experimental Data What Packages do I need? Specific to you data and analysis pipeline but for examples: Bioconductor Workshops Bioconductor Workflows Main types of Annotation Packages Gene centric AnnotationDbi packages: Organism: org.Mm.eg.db. Technology/Platform: hgu133plus2.db. GeneSets and Pathway (biology level): GO.db or KEGG.db .db packages can be queried with sql or accessed using annotation package (totable, get, mget) Genome centric GenomicFeatures packages: Transriptome level: TxDb.Hsapiens.UCSC.hg19.knownGene Generic features: Can generate via GenomicFeatures biomaRt: Query web-based `biomart resource for genes, sequence, SNPs, and etc. See /help/course-materials/2011/BioC2011/LabStuff/AnnotationSlidesBioc2011.pdf Bioconductor resources Mailing List (sign up for daily digest) Documentation, workshop/course material online Slides from talks, pdf of tutorials, R code Help available for each software package Each package MUST contain vignette (howto)? Other resources ww.R Vignette Tutorials, provide worked example of package Required in Bioconductor packages Written in Sweave (Leisch, 2002). LATEX dynamic reports in which R code is embedded and executable All R code in vignette is checked (and executed) by R CMD check /docs/vignettes.html library(Biobase) library(GOstats) # Load package of interest openVignette() S4 classes and ExpressionSet Within Bioconductor, you will encounter packages are structured around S4 object-oriented programming proposed b