Bioconductor

Release News

• 3.7 release
• 3.6 release
• 3.5 release

Github mirror

• https://support.bioconductor.org/p/68824/ Announcement (Update: it is dead)

Package source

• R > create Bioconductor repository

BiocManager from CRAN

The reason for using BiocManager instead of biocLite() is mostly to stop sourcing an R script from URL which isn’t so safe. So biocLite() should not be recommended anymore.

It allows to have multiple versions of Bioconductor installed on the same computer. For example, R 3.5 works with Bioconductor 3.7 and 3.8.

On the other hand, setRepositories(ind=1:4) and install.packages() still lets you install Bioconductor packages.

Hacking Bioconductor

BioCExplorer

Explore Bioconductor packages more nicely

source("https://bioconductor.org/biocLite.R")
biocLite("BiocUpgrade")
biocLite("biocViews")
devtools::install_github("seandavi/BiocPkgTools")
devtools::install_github("shians/BioCExplorer")
library(BioCExplorer)
bioc_explore()

Annotation packages

• http://bioconductor.org/help/course-materials/2012/SeattleFeb2012/Annotation.pdf
• https://bioconductor.org/help/course-materials/2017/CSAMA/lectures/1-monday/lecture-04-a-annotation-intro/lecture-04a-annotation-intro.html
• Making and Utilizing TxDb Objects
• Genomic Annotation Resources Introduction to using gene, pathway, gene ontology, homology annotations and the AnnotationHub. Access GO, KEGG, NCBI, Biomart, UCSC, vendor, and other sources.
  • AnnotationHub
  • OrgDb
  • TxDb
  • OrganismDb
  • BSgenome
  • biomaRt
• http://genomicsclass.github.io/book/pages/bioc1_annoCheat.html

Some packages

Biostrings

• Find the location of a particular sequence. ?vmatchPattern
• https://www.bioconductor.org/help/course-materials/2011/BioC2011/LabStuff/BiostringsBSgenomeOverview.pdf

library(Biostrings) 
library(BSgenome.Hsapiens.UCSC.hg19) 
vmatchPattern("GCGATCGC", Hsapiens)

plyranges

http://bioconductor.org/packages/devel/bioc/vignettes/plyranges/inst/doc/an-introduction.html

Misc

Package release history

https://support.bioconductor.org/p/69657/

Search the DESCRIPTION file (eg. VariantAnnotation package) in github and the release information can be found there.