RGMQL

DOI: 10.18129/B9.bioc.RGMQL    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see RGMQL.

GenoMetric Query Language for R/Bioconductor

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RGMQL")

For older versions of R, please refer to the appropriate Bioconductor release.

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, ImmunoOncology, Infrastructure, Network, SingleCell, Software
Version	1.4.1
In Bioconductor since	BioC 3.7 (R-3.5) (1.5 years)
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
Links To Me
Build Report

Package Archives

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

Source Package	RGMQL_1.4.1.tar.gz
Windows Binary	RGMQL_1.4.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	RGMQL_1.3.0.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	https://bioconductor.org/packages/RGMQL/
Package Downloads Report	Download Stats