Bioconductor: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
| Line 38: | Line 38: | ||
== Workflow == | == Workflow == | ||
=== [https://www.bioconductor.org/help/workflows/high-throughput-sequencing/ Using Bioconductor for Sequence Data] === | === [https://www.bioconductor.org/help/workflows/high-throughput-sequencing/ Using Bioconductor for Sequence Data] === | ||
== Misc == | |||
=== Package release history === | |||
https://support.bioconductor.org/p/69657/ | |||
Search the DESCRIPTION file (eg. [https://github.com/Bioconductor/VariantAnnotation/commits/master/DESCRIPTION VariantAnnotation] package) in github and the release information can be found there. | |||
Revision as of 15:58, 10 January 2018
Github Mirrors
- https://support.bioconductor.org/p/68824/ Announcement
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
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.