Bioconductor

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Revision as of 13:35, 17 April 2018 by Brb (talk | contribs) (→‎Misc)
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Github Mirrors

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

Find the location of a particular sequence. ?vmatchPattern

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

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.