SRAdb

A compilation of metadata from NCBI SRA and tools

Bioconductor version: 2.8

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 or sra-lite files 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 <zhujack at mail.nih.gov>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("SRAdb")

Documentation

PDF R Script Using SRAdb to Query the Sequence Read Archive
PDF   Reference Manual

Details

biocViews Infrastructure, HighThroughputSequencing, DataImport
Depends RSQLite (>= 0.8-4), graph, RCurl
Imports GEOquery
Suggests Rgraphviz
System Requirements
License Artistic-2.0
URL http://watson.nci.nih.gov/
Depends On Me
Imports Me
Suggests Me
Version 1.6.0
Since Bioconductor 2.6 (R-2.11)

Package Downloads

Package Source SRAdb_1.6.0.tar.gz
Windows Binary SRAdb_1.6.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary SRAdb_1.6.0.tgz
Package Downloads Report Download Stats

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