SRAdb

DOI: 10.18129/B9.bioc.SRAdb  

A compilation of metadata from NCBI SRA and tools

Bioconductor version: Release (3.16)

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. fastq and sra files can be downloaded for doing alignment locally. Beside ftp protocol, the SRAdb has funcitons supporting fastp protocol (ascp from Aspera Connect) for faster downloading large data files over long distance. 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>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SRAdb")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SRAdb")

 

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

Details

biocViews	DataImport, Infrastructure, Sequencing, Software
Version	1.60.0
In Bioconductor since	BioC 2.6 (R-2.11) (13 years)
License	Artistic-2.0
Depends	RSQLite, graph, RCurl
Imports	GEOquery
LinkingTo
Suggests	Rgraphviz
SystemRequirements
Enhances
URL
BugReports	https://github.com/zhujack/SRAdb/issues/new
Depends On Me
Imports Me
Suggests Me	parathyroidSE
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	SRAdb_1.60.0.tar.gz
Windows Binary	SRAdb_1.60.0.zip (64-bit only)
macOS Binary (x86_64)	SRAdb_1.60.0.tgz
macOS Binary (arm64)	SRAdb_1.60.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SRAdb
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SRAdb
Bioc Package Browser	https://code.bioconductor.org/browse/SRAdb/
Package Short Url	https://bioconductor.org/packages/SRAdb/
Package Downloads Report	Download Stats