Difference between revisions of "BioConductor/R framework"
From Organic Design wiki
m (→Accessing Bioconductor) |
m |
||
| Line 1: | Line 1: | ||
__NOTOC__ | __NOTOC__ | ||
| − | =====What is | + | =====What is BioConductor? (''http://www.bioconductor.org'')===== |
| − | * | + | *BioConductor is an open source development software project |
*Provides tools for analysis and comprehension of genomic data | *Provides tools for analysis and comprehension of genomic data | ||
*Extensively for Affymetrix and cDNA microarray technologies | *Extensively for Affymetrix and cDNA microarray technologies | ||
| Line 15: | Line 15: | ||
---- | ---- | ||
| − | ===== | + | =====BioConductor Goals===== |
The broad goals of the project are: | The broad goals of the project are: | ||
| Line 47: | Line 47: | ||
---- | ---- | ||
=====Accessing Bioconductor===== | =====Accessing Bioconductor===== | ||
| − | * | + | *BioConductor tools are accessed using the R programming language |
*R is a programming environment for statistical computing and graphics | *R is a programming environment for statistical computing and graphics | ||
*Initially written by Robert Gentleman and Ross Ihaka (''[http://en.wikipedia.org/wiki/University_of_Auckland Auckland University]'') | *Initially written by Robert Gentleman and Ross Ihaka (''[http://en.wikipedia.org/wiki/University_of_Auckland Auckland University]'') | ||
| Line 77: | Line 77: | ||
==TODO== | ==TODO== | ||
| − | * | + | *BioConductor resources/vignettes(including downloading) |
| − | * | + | *BioConductor basics (any resources for limma out there?) |
*usingR-2.pdf Chapter 1 → Starting up. | *usingR-2.pdf Chapter 1 → Starting up. | ||
*MGEDI → installing R/Bioconductor p30 - p34 (documentation/help) | *MGEDI → installing R/Bioconductor p30 - p34 (documentation/help) | ||
Revision as of 00:54, 16 March 2006
What is BioConductor? (http://www.bioconductor.org)
- BioConductor is an open source development software project
- Provides tools for analysis and comprehension of genomic data
- Extensively for Affymetrix and cDNA microarray technologies
- The project started in the autumn of 2001
- Includes 23 core collaborating developers
- Project Growth
- v1.0: May 2nd, 2002, 15 packages
- v1.1: November 18th, 2002, 20 packages.
- v1.2: May 28th, 2003, 30 packages.
- v1.3 Oct 29th 2003, 49 Packages
- v1.4 May 18 2004, 82 Packages
- v1.5 Nov 1st, 2004, 98 Packages
BioConductor Goals
The broad goals of the project are:
- To enable sound and powerful statistical analyses in genomics
- To provide a computing platform that allows the rapid design and deployment of high-quality software
- To develop a computing environment for both biologists and statisticians
- Promote high-quality dynamic documentation and reproducible research
- Using LATEX, the Sweave system and tcl/tk to deliver interactive step by step pdf tutorials, e.g.
library(tkWidgets) vExplorer()
Object oriented class method design (OOP)
- Organized approach to handling large amounts of experimental data
- Class structure encapsulates the data required for microarray analysis → object
- Allows efficient representation and manipulation (including subsetting) of data from many microarray slides in an experiment
- A method is a function that performs an action on data (objects) throughout analysis
Advantages
- Newest cutting edge statistical methods available
- Modern programming language
- Powerful graphical tools available
- Its freely available
Disadvantages
- Steep learning curve
- Need to have experience programming in the R programming environment (http://www.r-project.org)
- Like all software there are bugs
Accessing Bioconductor
- BioConductor tools are accessed using the R programming language
- R is a programming environment for statistical computing and graphics
- Initially written by Robert Gentleman and Ross Ihaka (Auckland University)
- Download R from a comprehensive R archive network (CRAN) mirror (http://cran.stat.auckland.ac.nz)
- Install R (available for Unix, Windows, and Mac OS X)
- R version 2.2.1 has been released on 2005-12-20
- R is the environment used to design and distribute software:
- Locally downloaded files
- Via the internet e.g. commands in R:
# Setting proxy variable # Downloading installation script
getBioC() # Running script
Installing vs loading packages
- Packages only need to be installed once onto a computer
- Packages must be loaded with each new R session
- The R function library is used to load packages e.g. command in R:
library(limma) #Installs the limma package
Documentation and Help
- R manuals and tutorials are available from the R website or on-line in an R session
- R on-line help system, detailed high quality on-line documentation, available in text, HTML, PDF, and LATEX formats.
- Frequently asked questions Bioconductor / R
- Email news lists for Bioconductor / R
- Note: Read the posting guides before submitting questions
TODO
- BioConductor resources/vignettes(including downloading)
- BioConductor basics (any resources for limma out there?)
- usingR-2.pdf Chapter 1 → Starting up.
- MGEDI → installing R/Bioconductor p30 - p34 (documentation/help)
