Bioconductor: Difference between revisions

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** BSgenome
** BSgenome
** biomaRt
** biomaRt
* http://genomicsclass.github.io/book/pages/bioc1_annoCheat.html


=== Gene centric ===
=== Gene centric ===

Revision as of 13:03, 1 October 2017

Github Mirrors

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

Annotation packages

Gene centric

Genomic centric

Web based

Workflow

Using Bioconductor for Sequence Data