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

BMC Bioinformatics

Volumn 14, Issue 1, 2013, Pages

  Zhu, Yuelin ^a,b   Stephens, Robert M ^b   Meltzer, Paul S ^a   Davis, Sean R ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b SAIC FREDERICK INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APPLIED BIOSYSTEMS; FULL-TEXT SEARCH; GENOME BROWSERS; GENOMICS; ILLUMINA; INTEGRATED FRAMEWORKS; LOCAL ANALYSIS; NEXT-GENERATION SEQUENCING; PUBLIC REPOSITORIES; QUERY RESULTS; SOLID SYSTEMS;

GENES; QUERY PROCESSING;

METADATA;

ARTICLE; COMPUTER PROGRAM; GENOMICS; HIGH THROUGHPUT SEQUENCING; METHODOLOGY; NUCLEIC ACID DATABASE;

DATABASES, NUCLEIC ACID; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; SOFTWARE;

EID: 84872274753     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-19     Document Type: Article

References (5)

1. The NCBI Sequence Read Archive. , http://www.ncbi.nlm.nih.gov/sra
2. R Core Team R: A Language and Environment for Statistical Computing 2012, R Foundation for Statistical Computing, Vienna, Austria, [phttp://www.R-project.org/]. [ISBN 3-900051-07-0], R Core Team.
3. Gentleman R, Carey V, Bates D, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5(10):R80. 10.1186/gb-2004-5-10-r80, 545600, 15461798.
4. Robinson J, Thorvaldsdóttir H, Winckler W, Guttman M, Lander E, Getz G, Mesirov J. Integrative genomics viewer. Nat Biotechnol 2011, 29:24-26. 10.1038/nbt.1754, 3346182, 21221095.
5. James DA, Falcon S. RSQLite: SQLite interface for R 2012, http://CRAN.R-project.org/package=RSQLite. [R package version 0.11.2].