DAVIDWebService-package: An R Package for retrieving data from DAVID into R objects using Web Services
Description
Tools for retrieving data from the Database for
Annotation, Visualization and Integrated Discovery
(DAVID) using Web Services into R objects. This package
offers the main functionalities of DAVID website
including:
- Connectivity:
- upload
gene/background list/s, change gene/background position,
select current specie/s, select annotations, etc. from
R.
- Exploration:
- native R objects of submitted
Gene List, Annotation Category Summary, Gene/Term
Clusters, Functional Annotation Chart and Functional
Annotation Tables. In addition it offers the usual
many-genes-to-many-terms visualization and induced Gene
Ontology direct acyclic graph GOstats-based conversion
method, in order to visualize GO structure.
References
- The Database for Annotation,
Visualization and Integrated Discovery
(david.abcc.ncifcrf.gov)
- Xiaoli Jiao, Brad T.
Sherman, Da Wei Huang, Robert Stephens, Michael W.
Baseler, H. Clifford Lane, Richard A. Lempicki, DAVID-WS:
A Stateful Web Service to Facilitate Gene/Protein List
Analysis Bioinformatics 2012
doi:10.1093/bioinformatics/bts251
- Huang, D.
W.; Sherman, B. T.; Tan, Q.; Kir, J.; Liu, D.; Bryant,
D.; Guo, Y.; Stephens, R.; Baseler, M. W.; Lane, H. C. &
Lempicki, R. A DAVID Bioinformatics Resources: expanded
annotation database and novel algorithms to better
extract biology from large gene lists. Nucleic Acids Res,
Laboratory of Immunopathogenesis and Bioinformatics,
SAIC-Frederick, Inc., National Cancer Institute at
Frederick, MD 21702, USA., 2007, 35, W169-W175
- Cristobal Fresno, Elmer A. Fernandez (2013)
RDAVIDWebService: a versatile R interface to DAVID,
Bioinformatics, 29(21), 2810-2811.,
http://bioinformatics.oxfordjournals.org/content/29/21/2810.