Package: RGMQL

 Type: Package

 Title: GenoMetric Query Language for R/Bioconductor

 Version: 1.5.0

 Author: Simone Pallotta, Marco Masseroli
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>

 Description: 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.

 License: Artistic-2.0

 URL: http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/

 Encoding: UTF-8
 LazyData: true

 RoxygenNote: 6.1.0

 Imports:
     httr,

     rJava,
     GenomicRanges,

     rtracklayer,
     data.table,
     utils,
     plyr,
     xml2,
     methods,
     S4Vectors,
     dplyr,

     stats,
     glue,
     BiocGenerics

 Depends:

     R(>= 3.4.2), RGMQLlib

 VignetteBuilder: knitr

 Suggests: 

     BiocStyle,
     knitr,
     rmarkdown

 biocViews:
     Software,
     Infrastructure,
     DataImport,
     Network,

     ImmunoOncology,

     SingleCell
 Collate: 

     'AllClasses.R'
     'AllGenerics.R'

     'GMQLtoGRanges.R'
     'GRangesToGMQL.R'

     'S3Aggregates.R'
     'S3Cover-Param.R'
     'S3Distal.R'
     'S3Operator.R'

     'Utils.R'

     'evaluation-functions.R'

     'filter-extract-function.R'

     'gmql_cover.R'
     'gmql_difference.R'
     'gmql_extend.R'

     'gmql_group.R'

     'gmql_init.R'

     'gmql_join.R'
     'gmql_map.R'
     'gmql_materialize.R'
     'gmql_merge.R'
     'gmql_order.R'
     'gmql_project.R'
     'gmql_read.R'
     'gmql_select.R'
     'gmql_union.R'

     'onLoad.R'

     'ordering-functions.R'
     'web-services.R'