CRAN
GREP2 1.0.1
GEO RNA-Seq Experiments Processing Pipeline
Released Jul 25, 2018 by Naim Al Mahi
This package cannot yet be used with Renjin it depends on other packages which are not available: org.Rn.eg.db, org.Mm.eg.db, org.Hs.eg.db, AnnotationDbi, GEOquery, GenomicFeatures, Biobase, EnsDb.Rnorvegicus.v79, EnsDb.Mmusculus.v79, tximport, and EnsDb.Hsapiens.v86
Dependencies
RCurl rentrez 1.2.1 XML 3.98-1.16
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