Bioconductor: Difference between revisions
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== 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] === | ||
== Some packages == | |||
=== Biostrings === | |||
Find the location of a particular sequence. [https://www.rdocumentation.org/packages/Biostrings/versions/2.40.2/topics/matchPattern ?vmatchPattern] | |||
<syntaxhighlight lang='rsplus'> | |||
library(Biostrings) | |||
library(BSgenome.Hsapiens.UCSC.hg19) | |||
vmatchPattern("GCGATCGC", Hsapiens) | |||
</syntaxhighlight> | |||
== Misc == | == Misc == |
Revision as of 13:35, 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
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.