get_metadata

geo_series_acc

directory where the metadata files will be saved.

destdir

logical, whether to download GEO metadata only.
Default is FALSE. If TRUE, then SRA metadata will not be
downloaded.

geo_only

download method for GEOquery.
See <code>'download.file'</code> from R package <a rd-options="utils" href="/link/utils?package=GREP2&version=1.0.2&to=utils" data-mini-rdoc="utils::utils">utils</a> 
for details. Default is 'libcurl'.

download_method

Download metadata from GEO and SRA

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>.

Naim Al Mahi

GREP2

GEO RNA-Seq Experiments Processing Pipeline

Mario Medvedovic

get_metadata function

download method for GEOquery.
See <code>'download.file'</code> from R package <a rd-options='utils' href='utils'>utils</a> 
for details. Default is 'libcurl'.

get_metadata: Download metadata from GEO and SRA

Description

Usage

Arguments

Value

Examples