Bioconductor: Difference between revisions

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== Package source ==
== Package source ==
* [[R#To_create_Bioconductor_repository|R > create Bioconductor repository]]
* [[R#To_create_Bioconductor_repository|R > create Bioconductor repository]]
== [https://cran.r-project.org/web/packages/BiocManager/index.html 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.


== [https://github.com/Shians/BioCExplorer BioCExplorer] ==
== [https://github.com/Shians/BioCExplorer BioCExplorer] ==

Revision as of 09:25, 9 November 2018

Release News

Github mirror

Package source

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.

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()

BiocExplorer.png

Annotation packages

Gene centric

Genomic centric

Web based

Workflow

Using Bioconductor for Sequence Data

Some packages

Biostrings

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.