DAVIDWebService-package: An R Package for retrieving data from DAVID into R objects...

In RDAVIDWebService: An R Package for retrieving data from DAVID into R objects using Web Services API.

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.

Author(s)

Cristobal Fresno [e-mail] and Elmer A. Fernandez [e-mail]

References

1. The Database for Annotation, Visualization and Integrated Discovery (david.abcc.ncifcrf.gov)

2. 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

3. 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

4. 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.

RDAVIDWebService documentation built on Nov. 8, 2020, 8:05 p.m.