Bioconductor: Difference between revisions

Revision as of 12:35, 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.

@@ Line 38: / Line 38: @@
 == Workflow ==
 === [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 ==