GREP2: GEO RNA-Seq Experiments Processing Pipeline

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>.

Version: 1.0.1
Depends: R (≥ 3.4.0)
Imports: XML, rentrez, RCurl, GEOquery, Biobase, parallel, tximport, EnsDb.Hsapiens.v86, EnsDb.Rnorvegicus.v79, EnsDb.Mmusculus.v79, AnnotationDbi,,,, GenomicFeatures, utils
Suggests: knitr, rmarkdown
Published: 2018-07-25
Author: Naim Al Mahi [cre, aut], Mario Medvedovic [aut, ctb]
Maintainer: Naim Al Mahi <mahina at>
License: GPL-3
NeedsCompilation: no
SystemRequirements: SRAtoolkit, Salmon, Java, FastQC, MultiQC
Citation: GREP2 citation info
Materials: README
CRAN checks: GREP2 results


Reference manual: GREP2.pdf
Vignettes: Process GEO RNA-seq data using GREP2
Package source: GREP2_1.0.1.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel: not available
OS X binaries: r-release: not available, r-oldrel: not available
Old sources: GREP2 archive


Please use the canonical form to link to this page.