SRAdb

A compilation of metadata from NCBI SRA and tools

Bioconductor version: Release (2.7)

The Sequence Read Archive (SRA) is the largest public repository of sequencing data from the next generation of sequencing platforms including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, and others. However, finding data of interest can be challenging using current tools. SRAdb is an attempt to make access to the metadata associated with submission, study, sample, experiment and run much more feasible. This is accomplished by parsing all the NCBI SRA metadata into a SQLite database that can be stored and queried locally. Fulltext search in the package make querying metadata very flexible and powerful. SRA data files (sra or sra-lite) can be downloaded for doing alignment locally. The SQLite database is updated regularly as new data is added to SRA and can be downloaded at will for the most up-to-date metadata.

Author: Jack Zhu and Sean Davis

Maintainer: Jack Zhu

To install this package, start R and enter:

source("http:///biocLite.R")
biocLite("SRAdb")    

Documentation

PDF

R Script

Using SRAdb to Query the Sequence Read Archive

Reference Manual

Details

biocViews	Infrastructure, HighThroughputSequencing, DataImport
Depends	RSQLite, graph
Imports	RCurl, GEOquery
Suggests	Rgraphviz
System Requirements
License	Artistic-2.0
URL	http://watson.nci.nih.gov/
Depends On Me
Imports Me
Suggests Me
Version	1.4.1

Package Downloads

Package Source	SRAdb_1.4.1.tar.gz
Windows Binary	SRAdb_1.4.1.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	SRAdb_1.4.1.tgz
Package Downloads Report	Download Stats