SRAdb
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SRAdb.
A compilation of metadata from NCBI SRA and tools
Bioconductor version: 3.12
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>
citation("SRAdb")):
Installation
To install this package, start R (version "4.0") 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")| Using SRAdb to Query the Sequence Read Archive | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, Infrastructure, Sequencing, Software |
| Version | 1.52.0 |
| In Bioconductor since | BioC 2.6 (R-2.11) (14 years) |
| License | Artistic-2.0 |
| Depends | RSQLite, graph, RCurl |
| Imports | GEOquery |
| System Requirements | |
| URL | http://gbnci.abcc.ncifcrf.gov/sra/ |
| Bug Reports | https://github.com/seandavi/SRAdb/issues/new |
See More
| Suggests | Rgraphviz |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | parathyroidSE |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SRAdb_1.52.0.tar.gz |
| Windows Binary | SRAdb_1.52.0.zip |
| macOS 10.13 (High Sierra) | SRAdb_1.52.0.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 |
| Old Source Packages for BioC 3.12 | Source Archive |