Bioconductor

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