BioConductor.ppt
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1、BioConductor,Steffen Durinck Robert Gentleman Sandrine DudoitNovember 28, 2003 NETTAB Bologna,Outline,what is R what is Bioconductor packages getting and using Bioconductor,R,R is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S languag
2、e and environment which was developed at Bell Laboratories (formerly AT&T, now Lucent Technologies) by John Chambers and colleagues. R can be considered as a different implementation of S.,R,what sorts of things is R good at? there are very many statistical algorithms there are very many machine lea
3、rning algorithms visualization it is possible to write scripts that can be reused R is a real computer language,R,R supports many data technologies XML,database integration,SOAP R interacts with other languages C; FORTRAN; Perl; Python; Java R has good visualization capabilities R has a very active
4、development environment R is largely platform independent Unix; Windows; OSX,Overview of the Bioconductor Project,Bioconductor,Bioconductor is an open source and open development software project for the analysis of biomedical and genomic data. The project was started in the Fall of 2001 and include
5、s 23 core developers in the US, Europe, and Australia. R and the R package system are used to design and distribute software. Releases v 1.0: May 2nd, 2002, 15 packages. v 1.1: November 18th, 2002, 20 packages. v 1.2: May 28th, 2003, 30 packages. v 1.3: October 28th, 2003, 54 packages. ArrayAnalyzer
6、: Commercial port of Bioconductor packages in S-Plus.,Goals,Provide access to powerful statistical and graphical methods for the analysis of genomic data. Facilitate the integration of biological metadata (GenBank, GO, LocusLink, PubMed) in the analysis of experimental data. Allow the rapid developm
7、ent of extensible, interoperable, and scalable software. Promote high-quality documentation and reproducible research. Provide training in computational and statistical methods.,Bioconductor Packages,Bioconductor packages,Bioconductor software consists of R add-on packages. An R package is a structu
8、red collection of code (R, C, or other), documentation, and/or data for performing specific types of analyses. E.g. affy, cluster, graph, hexbin packages provide implementations of specialized statistical and graphical methods.,Bioconductor packages Release 1.3, October 28th, 2003,AnnBuilder Biocond
9、uctor annotation data package builder Biobase Biobase: Base functions for Bioconductor DynDoc Dynamic document tools MAGEML handling MAGEML documents MeasurementError.cor Measurement Error model estimate for correlation coefficient RBGL Test interface to boost C+ graph lib ROC utilities for ROC, wit
10、h uarray focus RdbiPgSQL PostgreSQL access Rdbi Generic database methods Rgraphviz Provides plotting capabilities for R graph objects Ruuid Ruuid: Provides Universally Unique ID values SAGElyzer A package that deals with SAGE libraries SNPtools Rudimentary structures for SNP data affyPLM affyPLM - P
11、robe Level Models Affy Methods for Affymetrix Oligonucleotide Arrays Affycomp Graphics Toolbox for Assessment of Affymetrix Expression Measures Affydata Affymetrix Data for Demonstration Purpose Annaffy Annotation tools for Affymetrix biological metadata Annotate Annotation for microarrays,Ctc Clust
12、er and Tree Conversion. daMA Efficient design and analysis of factorial two-colour microarray data Edd expression density diagnostics externalVector Vector objects for R with external storage factDesign Factorial designed microarray experiment analysis Gcrma Background Adjustment Using Sequence Info
13、rmation Genefilter Genefilter: filter genes Geneplotter Geneplotter: plot microarray data Globaltest Global Test Gpls Classification using generalized partial least squares Graph graph: A package to handle graph data structures Hexbin Hexagonal Binning Routines Limma Linear Models for Microarray Dat
14、a Makecdfenv CDF Environment Maker marrayClasses Classes and methods for cDNA microarray data marrayInput Data input for cDNA microarrays marrayNorm Location and scale normalization for cDNA microarray data marrayPlots Diagnostic plots for cDNA microarray data marrayTools Miscellaneous functions for
15、 cDNA microarrays,Bioconductor packages Release 1.3, October 28th, 2003,Bioconductor packages Release 1.3, October 28th, 2003,Matchprobes Tools for sequence matching of probes on arrays Multtest Multiple Testing Procedures ontoTools graphs and sparse matrices for working with ontologies Pamr Pam: pr
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