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 |
| 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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