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
- https://support.bioconductor.org/p/68824/ Announcement (Update: it is dead)
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()
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
Gene centric
Genomic centric
Web based
Workflow
Using Bioconductor for Sequence Data
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.