Bioconductor: Difference between revisions
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== Some packages == | == Some packages == | ||
=== Biostrings === | === Biostrings === | ||
Find the location of a particular sequence. [https://www.rdocumentation.org/packages/Biostrings/versions/2.40.2/topics/matchPattern ?vmatchPattern] | * Find the location of a particular sequence. [https://www.rdocumentation.org/packages/Biostrings/versions/2.40.2/topics/matchPattern ?vmatchPattern] | ||
* https://www.bioconductor.org/help/course-materials/2011/BioC2011/LabStuff/BiostringsBSgenomeOverview.pdf | |||
<syntaxhighlight lang='rsplus'> | <syntaxhighlight lang='rsplus'> | ||
library(Biostrings) | library(Biostrings) | ||
Revision as of 12:42, 17 April 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
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)
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.