The genbankr package is part of the Bioconductor ecosystem of R packages. As
such, it's primary splash page - including continuous integration and testing
badges - can be found here.
genbankr is a package which provides utilities to parse GenBank and GenPept
files into data structures which integrate with the Bioconductor ecosystem.
This package depends on the Bioconductor ecosystem of R packages. If you already have a version of Bioconductor (>=3.3) installed, you can do gthe following:
libary(BiocInstaller)
biocLite("genbankr")
If you do not currently have the Bioconductor core machinery installed, you can get the current or release version like so:
source("http://bioconductor.org/biocLite.R")
for release and
source("http://bioconductor.org/biocLite.R")
try(useDevel(TRUE))
For devel.
After doing one of the above (once), you can install genbankr as above, via
library(BiocInstaller)
biocLite("genbankr")
Note that Bioconductor is a sychronized development and release
platform, so release and development versions of Bioconductor packages
cannot be safely mixed in the same package (installation) library. Use switchr
or direct .libPaths management to maintain multiple side-by-side installations
if necessary.
To install directly from github (this will generally not be necessary
unless you intend to contribute to genbankr's development), do
source("http://bioconductor.org/biocLite.R")
try(useDevel(TRUE))
biocLite("gmbecker/genbankr")
The Bioconductor development repository will contain the latest development version of genbankr which has passed testing (lagged by about a day).
The primary workhorse function in genbankr is readGenBank(). To read a genbank
file, simply call this function on the downloaded file, or on a GBAccession object.
library(genbankr)
mygbk = readGenbank("gbkfile.gbk")
For a more complete discussion of how to use the genbankr package, please see
the compiled vignette here
Please post any usage questions about genbankr on the Bioconductor Support Site
here with the tag genbankr.
Bugs and feature requests can be filed as issues on this Github repository.
This project operates under the Contributor Covenenant Code of Coduct see here
The genbankr package is a part of the Bioconductor and rOpenSci projects.
 |
 |
|---|