DESCRIPTION

Package: GREP2
Type: Package
Title: GEO RNA-Seq Experiments Processing Pipeline
Version: 1.0.2
Authors@R: c(person("Naim Al", "Mahi", role = c("cre", "aut"),
				email = "mahina@mail.uc.edu"),
				person("Mario", "Medvedovic", role = c("aut", "ctb")))
Maintainer: Naim Al Mahi <mahina@mail.uc.edu>
Description: An R based pipeline to download and process Gene Expression Omnibus (GEO) RNA-seq data. 
    For a given GEO series accession ID, this pipeline generates metadata, 
    both gene and transcript level counts, and quality control (QC) report. 
	This package is mainly developed to process the GEO RNA-seq datasets 
	for the web platform GREIN. More details about GREP2 and GREIN can be 
	found here <doi:10.1101/326223>.
Depends: R (>= 3.4.0)
Imports: XML, rentrez, RCurl, GEOquery, Biobase, parallel, tximport, 
    EnsDb.Hsapiens.v86, EnsDb.Rnorvegicus.v79, EnsDb.Mmusculus.v79,
    AnnotationDbi, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, 
	GenomicFeatures, utils
Suggests: knitr, rmarkdown
SystemRequirements: SRAtoolkit, Salmon, Java, FastQC, MultiQC
URL: https://github.com/uc-bd2k/GREP2
BugReports: https://github.com/uc-bd2k/GREP2/issues
License: GPL-3
VignetteBuilder: knitr
LazyData: true
Encoding: UTF-8
RoxygenNote: 6.1.1