RGMQL

DOI: 10.18129/B9.bioc.RGMQL    

This is the development version of RGMQL; for the stable release version, see RGMQL.

GenoMetric Query Language for R/Bioconductor

Bioconductor version: Development (3.8)

This package brings the GenoMetric Query Language (GMQL) functionalities into the R environment. GMQL is a high-level, declarative language to manage heterogeneous genomic datasets for biomedical purposes, using simple queries to process genomic regions and their metadata and properties. GMQL adopts algorithms efficiently designed for big data using cloud-computing technologies (like Apache Hadoop and Spark) allowing GMQL to run on modern infrastructures, in order to achieve scalability and high performance. It allows to create, manipulate and extract genomic data from different data sources both locally and remotely. Our RGMQL functions allow complex queries and processing leveraging on the R idiomatic paradigm. The RGMQL package also provides a rich set of ancillary classes that allow sophisticated input/output management and sorting, such as: ASC, DESC, BAG, MIN, MAX, SUM, AVG, MEDIAN, STD, Q1, Q2, Q3 (and many others). Note that many RGMQL functions are not directly executed in R environment, but are deferred until real execution is issued.

Author: Simone Pallotta, Marco Masseroli

Maintainer: Simone Pallotta <simonepallotta at hotmail.com>

Citation (from within R, enter citation("RGMQL")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("RGMQL")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("RGMQL")

 

PDF R Script RGMQL: GenoMetric Query Language for R/Bioconductor
PDF   Reference Manual
Text   NEWS

Details

biocViews DataImport, Infrastructure, Network, SingleCell, Software
Version 1.1.0
License Artistic-2.0
Depends R (>= 3.4.2), RGMQLlib
Imports httr, rJava, GenomicRanges, rtracklayer, data.table, utils, plyr, xml2, methods, S4Vectors, dplyr, stats, glue, BiocGenerics
LinkingTo
Suggests BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package RGMQL_1.1.0.tar.gz
Windows Binary RGMQL_1.1.0.zip
Mac OS X 10.11 (El Capitan) RGMQL_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/RGMQL
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RGMQL
Package Short Url http://bioconductor.org/packages/RGMQL/
Package Downloads Report Download Stats

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