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== [https://github.com/Bioconductor-mirror Github | == Release News == | ||
* https://support.bioconductor.org/p/68824/ Announcement | * [http://bioconductor.org/news/bioc_3_7_release/ 3.7] release | ||
* [https://bioconductor.org/news/bioc_3_6_release/ 3.6] release | |||
* [https://bioconductor.org/news/bioc_3_5_release/ 3.5] release | |||
== [https://github.com/Bioconductor-mirror Github mirror] == | |||
* https://support.bioconductor.org/p/68824/ Announcement (Update: it is dead) | |||
== Package source == | |||
* [[R#To_create_Bioconductor_repository|R > create Bioconductor repository]] | |||
== [https://github.com/Shians/BioCExplorer BioCExplorer] == | == [https://github.com/Shians/BioCExplorer BioCExplorer] == | ||
Revision as of 11:35, 9 August 2018
Release News
Github mirror
- https://support.bioconductor.org/p/68824/ Announcement (Update: it is dead)
Package source
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.