ArrayExpress update—trends in database growth and links to data analysis tools

A pipeline for RNA-seq data processing and quality assessment

(2011) Angela Goncalves et al.   BIOINFORMATICS

The BioSample Database (BioSD) at the European Bioinformatics Institute

(2011) M. Gostev et al.   NUCLEIC ACIDS RESEARCH

The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments

(2011) M. Kapushesky et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Annotare--a tool for annotating high-throughput biomedical investigations and resulting data

(2010) R. Shankar et al.   BIOINFORMATICS

Modeling sample variables with an Experimental Factor Ontology

(2010) James Malone et al.   BIOINFORMATICS

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments

(2010) H. Parkinson et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Importing ArrayExpress datasets into R/Bioconductor

(2009) Audrey Kauffmann et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB

(2008) T. F. Rayner et al.   BIOINFORMATICS

Petabyte-scale innovations at the European Nucleotide Archive

(2008) G. Cochrane et al.   NUCLEIC ACIDS RESEARCH