Difference between revisions of "SRAdb"
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{{Bioinformatics application | {{Bioinformatics application | ||
|sw summary=R tool to query Short Read Archive and download data from it | |sw summary=R tool to query Short Read Archive and download data from it | ||
| + | |created by= Jack Zhu, Sean Davis | ||
| + | |created at=National Institutes of Health | ||
|language=R | |language=R | ||
}} | }} | ||
== Description == | == Description == | ||
<!-- Describe the application in the space below --> | <!-- Describe the application in the space below --> | ||
| + | High throughput sequencing technologies have very rapidly become standard tools in biology. The data that these machines generate are large, extremely rich. As such, the Sequence Read Archives (SRA) have been set up at NCBI in the United States, EMBL in Europe, and DDBJ in Japan to capture these data in public repositories in much the same spirit as MIAME-compliant microarray databases like NCBI GEO and EBI ArrayExpress. | ||
| + | Accessing data in SRA requires �nding it �rst. This R package provides a convenient and powerful framework to do just that. In addition, SRAdb features functionality to determine availability of sequence �les and to download �les of interest. | ||
| + | |||
| + | SRA does not currently store aligned reads or any other processed data that might rely on alignment to a reference genome. However, NCBI GEO does often contain aligned reads for sequencing experiments and the SRAdb package can help to provide links to these data as well. In combination with the GEOmetadb and GEOquery packages, these data are also, then, accessible. | ||
Revision as of 10:09, 20 September 2011
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Application data |
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| Created by | Jack Zhu, Sean Davis |
|---|---|
| Created at | National Institutes of Health |
| Maintained? | Maybe |
| Programming language(s) | R |
Summary: R tool to query Short Read Archive and download data from it
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Description
High throughput sequencing technologies have very rapidly become standard tools in biology. The data that these machines generate are large, extremely rich. As such, the Sequence Read Archives (SRA) have been set up at NCBI in the United States, EMBL in Europe, and DDBJ in Japan to capture these data in public repositories in much the same spirit as MIAME-compliant microarray databases like NCBI GEO and EBI ArrayExpress.
Accessing data in SRA requires �nding it �rst. This R package provides a convenient and powerful framework to do just that. In addition, SRAdb features functionality to determine availability of sequence �les and to download �les of interest.
SRA does not currently store aligned reads or any other processed data that might rely on alignment to a reference genome. However, NCBI GEO does often contain aligned reads for sequencing experiments and the SRAdb package can help to provide links to these data as well. In combination with the GEOmetadb and GEOquery packages, these data are also, then, accessible.
Links
References
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