Features/Bioconductor

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These libraries are
 
These libraries are
* affy
+
# affy
* affydata
+
# affydata
* affyPLM
+
# affyPLM
* annaffy
+
# annaffy
* annotate
+
# annotate
* Biobase
+
# Biobase
* Biostrings
+
# Biostrings
* DynDoc
+
# DynDoc
* gcrma
+
# gcrma
* genefilter
+
# genefilter
* geneplotter
+
# geneplotter
* hgu95av2.db
+
# hgu95av2.db
* limma
+
# limma
* marray
+
# marray
* matchprobes
+
# matchprobes
* multtest
+
# multtest
* ROC
+
# ROC
* vsn
+
# vsn
* xtable
+
# xtable
* affyQCReport.
+
# affyQCReport.
  
 
The problem is that those libraries can have a high amount of dependencies.
 
The problem is that those libraries can have a high amount of dependencies.

Revision as of 15:39, 19 July 2008

Contents

Bioconductor

Summary

Make |Bioconductor available for Fedora

"Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data."

Owner

  • Name: PierreYvesChibon

Current status

  • Targeted release: Fedora11
  • Last updated: 19 July 2008
  • Percentage of completion: 10%

Detailed Description

Bioconductor is a large R libraries repository widely used in bioinformatics for statistical analysis of genomic data.

Benefit to Fedora

Widely used packaging Bioconductor would offer a good way to promote Fedora as desktop platform for bioinformaticians.

In addition it could also be promoted in RHEL since some servers running RHEL are used to process the analysis that bioconductor offers.

Scope

Bioconductors contains around 300 packages, not all will be packaged in Fedora (at least not at first). I think for the feature the basis packages of bioconductor should be done.

Bioconductor has its own installation script in R which enable to install the basis libraries of Bioconductor.

These libraries are

  1. affy
  2. affydata
  3. affyPLM
  4. annaffy
  5. annotate
  6. Biobase
  7. Biostrings
  8. DynDoc
  9. gcrma
  10. genefilter
  11. geneplotter
  12. hgu95av2.db
  13. limma
  14. marray
  15. matchprobes
  16. multtest
  17. ROC
  18. vsn
  19. xtable
  20. affyQCReport.

The problem is that those libraries can have a high amount of dependencies.

Test Plan

Install the RPMs and test them

User Experience

The users should be able to download the libraries and start to work with it without problem.

In addition it might be interesting to create a package group Bioconductor, which allows to install those packages and their dependencies all at once.

Dependencies

They are included in the R libraries, most of them are in Bioconductor, some can be in the CRAN repository.

The question of the metadata and experiment data packages should be taken into account. These are heavy packages which do not evolve lot between release. Two of them are incorporated already into Fedora, they brought the question of inheritance between the version.

Contingency Plan

None

Planning

  1. Find interested contributors
  2. Get a clear view on the amount of packages that have to be done
  3. Package and review them

Documentation

Release Notes

None