Bioconductor: Difference between revisions

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== [https://github.com/Bioconductor-mirror Github Mirrors] ==
== [https://github.com/Bioconductor-mirror Github Mirrors] ==
* https://support.bioconductor.org/p/68824/ Announcement
* https://support.bioconductor.org/p/68824/ Announcement
== [http://watson.nci.nih.gov/bioc_mirror/ 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
<pre>
http://www.bioconductor.org/packages/release/bioc/html/Biobase.html
->
http://watson.nci.nih.gov/bioc_mirror/packages/release/bioc/html/Biobase.html
</pre>
and the hgu133plusdb is
<pre>
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
</pre>
and the experiment data package like pasilla
<pre>
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
</pre>
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
<pre>
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
</pre>
and the 'MASS' package is
<pre>
http://cran.r-project.org/web/packages/MASS/index.html
->
http://watson.nci.nih.gov/cran_mirror/web/packages/MASS/index.html
</pre>


== [https://github.com/Shians/BioCExplorer BioCExplorer] ==
== [https://github.com/Shians/BioCExplorer BioCExplorer] ==

Revision as of 15:38, 5 January 2018

Github Mirrors

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()

BiocExplorer.png

Annotation packages

Gene centric

Genomic centric

Web based

Workflow

Using Bioconductor for Sequence Data

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