https://github.com/bioconductor/googlegenomics

An R package for Google Genomics API queries.
https://github.com/bioconductor/googlegenomics

bioconductor-packages core-package retired-package

Last synced: 9 months ago
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An R package for Google Genomics API queries.

• Host: GitHub
• URL: https://github.com/bioconductor/googlegenomics
• Owner: Bioconductor
• License: apache-2.0
• Created: 2014-04-29T17:41:58.000Z (about 12 years ago)
• Default Branch: devel
• Last Pushed: 2023-03-15T20:25:05.000Z (about 3 years ago)
• Last Synced: 2024-05-09T07:46:37.036Z (about 2 years ago)
• Topics: bioconductor-packages, core-package, retired-package
• Language: R
• Homepage:
• Size: 379 KB
• Stars: 42
• Watchers: 40
• Forks: 26
• Open Issues: 8
• Metadata Files:
  • Readme: README.rst
  • Contributing: CONTRIBUTING.rst
  • License: LICENSE

Awesome Lists containing this project

README

          
GoogleGenomics  |Build Status|_

===============================

.. |Build Status| image:: http://img.shields.io/travis/Bioconductor/GoogleGenomics.svg?style=flat

.. _Build Status: https://travis-ci.org/Bioconductor/GoogleGenomics

.. role:: r(code)

   :language: r

.. role:: sh(code)

   :language: sh

This R client fetches reads and variants data from the `Google Genomics API`_

and provides converters to obtain `Bioconductor`_ S4 classes like GAlignments,

and GRanges and VRanges.

.. _Google Genomics API: https://cloud.google.com/genomics

.. _Bioconductor: http://www.bioconductor.org/

.. _gRPC: https://grpc.io/

Installing

----------

Use the Bioconductor repositories to install this package.

If you have `gRPC`_ installed, you will be able to access the entire v1

Google Genomics API through the :r:`callGRPCMethod` function provided in

the package and use more performant reads and variant search methods.

Without gRPC support, you will still be able to query reads and variants;

see the vignettes for sample usage.

* [Optional] Installing gRPC

  See `our guide on gRPC `_.

* Installing R package

  .. code:: r

    source("http://bioconductor.org/biocLite.R")

    useDevel(TRUE) # Skip this step if you do not want the devel version.

    biocLite("GoogleGenomics")  # If gRPC is not installed.

    biocLite("GoogleGenomics", type="source")  # If gRPC is installed.

    library(GoogleGenomics)

Authentication

--------------

Call :r:`authenticate` to set up credentials. Check the function

documentation for details on various available options. The function will

return :r:`TRUE` on successful authentication.

Examples

--------

See the following examples for more detail:

* `Working with Reads `_

* `Working with Variants `_

* `Variant Annotation Comparison Test `_

* and also the `integration tests <./tests/testthat>`_

Project status

--------------

The package is integrated with gRPC when available on the system where the

package was built. With gRPC support, the entire v1 API is accessible.

Without gRPC support, this package can be used to search for reads and

variants, and convert them to various Bioconductor formats.