SRAdb statistics

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SRAdb specifications

Information


Unique identifier OMICS_01032
Name SRAdb
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.42.2
Stability Stable
Requirements
GEOquery, RSQLite, graph, RCurl, Rgraphviz
Maintained Yes

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Documentation


Maintainer


  • person_outline Jack Zhu <>

Publication for SRAdb

SRAdb in publications

 (5)
PMCID: 5203714
PMID: 28038678
DOI: 10.1186/s13059-016-1118-6

[…] platforms because of their ubiquity and high base-calling accuracy. specifically, the samples we aligned were obtained by querying the sra metadata sqlite database of the r/bioconductor package sradb [] as of april 2015 for all illumina-sequenced human rna-seq samples., in the remainder of this paper, we use the term “annotation” to refer to junctions from the union of transcripts across […]

PMCID: 4900452
PMID: 27279223
DOI: 10.1038/nature18297

[…] differences for a large number of genes. the following parameters were used for the test: groupings were not preserved for randomizations, both sides, 250 randomizations, fdr of 1% and s0 of 0.1., a sradb r/bioconductor query of ncbi’s short read archive (sra) with search term “marine sediment” yielded 130 shotgun metagenomes. after downloading and converting the sra files to fastq format, […]

PMCID: 5429001
PMID: 27142216
DOI: 10.1093/bib/bbw036

[…] and released as chip-seq experiments. each chip-seq sample in geo is linked to the sequence read archive (sra), a public repository of high-throughput sequencing (hts) raw data and their metadata. sradb [] is an r/bioconductor package collecting sra metadata into an sqlite database and providing the user a way to quickly query samples metadata and eventually download the associated sequence […]

PMCID: 4425880
PMID: 25960871
DOI: 10.1186/s13742-015-0064-7

[…] repository sequence read archive (sra) in order to ascertain the level of annotation of important sequencing steps in submissions to the database. using sql relational database queries (using the sradb sqlite database generated by the bioconductor consortium) to search for keywords commonly occurring in key preparatory protocol steps partitioned over studies, we found that 7.10%, 5.84% […]

PMCID: 4510819
PMID: 25690415
DOI: 10.1002/pmic.201400392

[…] data such as the arrayexpress database at european bioinformatics institute (arrayexpress package []), ncbi gene expression omnibus (geo) (geoquery package []), and sequence read archive (sra) (sradb package []) public repositories. such mechanisms that enable distribution and access the growing number of well-curated and publicly available datasets are critical in facilitating access, […]


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SRAdb institution(s)
Genetics Branch, National Cancer Institute, National Institutes of HealthBethesda, MD, USA

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