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, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, 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 mail.uc.edu>
BugReports: https://github.com/uc-bd2k/GREP2/issues
License: GPL-3
URL: https://github.com/uc-bd2k/GREP2
NeedsCompilation: no
SystemRequirements: SRAtoolkit, Salmon, Java, FastQC, MultiQC
Citation: GREP2 citation info
Materials: README
CRAN checks: GREP2 results

Downloads:

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

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