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RGMQL

GenoMetric Query Language for R/Bioconductor


Bioconductor version: Release (3.18)

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 [aut, cre], Marco Masseroli [aut]

Maintainer: Simone Pallotta <simonepallotta at hotmail.com>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("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")
RGMQL: GenoMetric Query Language for R/Bioconductor HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataImport, ImmunoOncology, Infrastructure, Network, SingleCell, Software
Version 1.22.0
In Bioconductor since BioC 3.7 (R-3.5) (6 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
System Requirements
URL http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/
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Package Archives

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

Source Package RGMQL_1.22.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/RGMQL
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RGMQL
Bioc Package Browser https://code.bioconductor.org/browse/RGMQL/
Package Short Url https://bioconductor.org/packages/RGMQL/
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