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SRAdb | Query and use public next-generation sequencing data from within R

Helps to make queries of the metadata associated with SRA submission, study, sample, experiment and to run more robust and precise, and to make access to sequencing data in the SRA easier. All the SRA metadata have been parsed into a SQLite database that is routinely updated and can be easily distributed. The SRAdb R/Bioconductor package then utilizes this SQLite database for querying and accessing metadata. Full text search functionality makes querying metadata very flexible and powerful. Fastq files associated with query results can be downloaded easily for local analysis. It also includes an interface from R to a popular genome browser, the Integrated Genomics Viewer.

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SRAdb forum

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SRAdb classification

SRAdb specifications

Unique identifier:
OMICS_01032
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
Artistic License version 2.0
Stability:
Stable
Software type:
Package/Module
Restrictions to use:
None
Programming languages:
R
Computer skills:
Advanced
Maintained:
Yes

SRAdb distribution

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No versioning.

SRAdb support

Documentation

Maintainer

Credits

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Publications

Institution(s)

Genetics Branch, National Cancer Institute, National Institutes of HealthBethesda, MD, USA

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