Resources

Development and Daily build system

• Software and Annotation data packages are build daily
• Experiment data packages are build just twice a week: Wednesdays and Saturdays.
• Bioconductor build/check results is available at here and Build System RSS Feeds is also available. Annotations packages such as GO.db do not have build reports
• Search Bioconductor code without downloading packages at Bioconductor Git Mirror
• Download stats for Bioconductor Software packages are here
• Dashboard

Source code

To view SVN source code, visit https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ and type

username: readonly
password: readonly

• There are always two branches of Bioconductor packages. For example, in the 3.0 branch, the release packages are accessible at: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/
• The devel version of packages are at: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/
• For the release version of experiment packages, they are accessible at: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_0/experiment/pkgs/
• Similarly, the devel version of experiment packages are available at: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/

Package handling

source("http://bioconductor.org/biocLite.R")
biocLite()

source("http://bioconductor.org/biocLite.R")
biocLite("BiocUpgrade")

source("http://bioconductor.org/biocLite.R")
useDevel()
biocLite("PACKAGENAME")

Organism packages

There are no organism-centric genomewide annotation packages (org.XX.eg.db) for horse and sheep as of February 2015. Available domestic animal species are cattle, chiken, and pig. These packages are anchored at Entrez gene identifiers, but not Ensembl gene identifiers.

Short URL

This can be used in publications or grant proposals to reference Bioconductor packages.

• This page http://bioconductor.org/packages/meshr/ lands on http://bioconductor.org/packages/release/bioc/html/meshr.html
• This page http://bioconductor.org/packages/release/meshr/ lands on http://bioconductor.org/packages/release/bioc/html/meshr.html
• This page http://bioconductor.org/packages/devel/meshr/ lands on http://bioconductor.org/packages/devel/bioc/html/meshr.html
• This page http://bioconductor.org/packages/3.0/meshr/ lands on http://bioconductor.org/packages/3.0/bioc/html/meshr.html

© 2015 Gota Morota with help from RStudio and BiocStyle