selcenari/genbankr

Package

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.

Introduction

genbankr is a package which provides utilities to parse GenBank and GenPept files into data structures which integrate with the Bioconductor ecosystem.

Installation

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).

Basic usage

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

Help and filing bugs

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.

Code of Conduct

This project operates under the Contributor Covenenant Code of Coduct see here

Package Affiliations

The genbankr package is a part of the Bioconductor and rOpenSci projects.

selcenari / genbankr