Bioconductor: Difference between revisions
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== Annotation packages == | == Annotation packages == |
Revision as of 16:32, 5 January 2018
Github Mirrors
- https://support.bioconductor.org/p/68824/ Announcement
NIH mirror
We can safely replace http://www.bioconductor.org/ with http://watson.nci.nih.gov/bioc_mirror/.
For example, the 'Biobase' url in the original and nih mirror can be found in
http://www.bioconductor.org/packages/release/bioc/html/Biobase.html -> http://watson.nci.nih.gov/bioc_mirror/packages/release/bioc/html/Biobase.html
and the hgu133plusdb is
http://www.bioconductor.org/packages/release/data/annotation/html/hgu133plus2.db.html -> http://watson.nci.nih.gov/bioc_mirror/packages/release/data/annotation/html/hgu133plus2.db.html
and the experiment data package like pasilla
http://www.bioconductor.org/packages/release/data/experiment/html/pasilla.html -> http://watson.nci.nih.gov/bioc_mirror/packages/release/data/experiment/html/pasilla.html
For R software, the NIH mirror is http://watson.nci.nih.gov/cran_mirror. So for example, the R v3.2.1 url in main CRAN and NIH is
http://cran.r-project.org/bin/windows/base/R-3.2.1-win.exe -> http://watson.nci.nih.gov/cran_mirror/bin/windows/base/R-3.2.1-win.exe
and the 'MASS' package is
http://cran.r-project.org/web/packages/MASS/index.html -> http://watson.nci.nih.gov/cran_mirror/web/packages/MASS/index.html
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