RBiopaxParser-an R package to parse, modify and visualize BioPAX data

Bioinformatics

Volumn 29, Issue 4, 2013, Pages 520-522

  Kramer, Frank ^a   Bayerlová, Michaela ^a   Klemm, Florian ^a   Bleckmann, Annalen ^a   Beißbarth, Tim ^a  

^a UNIVERSITY MEDICAL CENTER GÖTTINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; COMPUTER GRAPHICS; COMPUTER PROGRAM; FACTUAL DATABASE; GENOMICS; LINGUISTICS; SIGNAL TRANSDUCTION;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; DATABASES, FACTUAL; GENOMICS; MODELS, BIOLOGICAL; SIGNAL TRANSDUCTION; SOFTWARE; VOCABULARY, CONTROLLED;

MLCS; MLOWN;

EID: 84874305241     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts710     Document Type: Article

References (13)

1. Bader, G.D. et al. (2006) Pathguide: a pathway resource list. Nucleic Acids Res., 34, D504-D506.
2. Beißbarth, T. (2006) Interpreting experimental results using gene ontologies. Methods Enzymol., 411, 340-352.
3. Bender, C. et al. (2011) Inferring signaling networks from longitudinal data using sampling based approaches in the R-package 'ddepn'. BMC Bioinformatics, 12, 291.
4. Carey, V.J. (2005) Network structures and algorithms in Bioconductor. Bioinformatics, 21, 135-136.
5. Croft, D. et al. (2010) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res., 39, D691-D697.
6. Demir, E. et al. (2010) The BioPAX community standard for pathway data sharing. Nat. Biotechnol., 28, 935-942.
7. Fröhlich, H. et al. (2008) Estimating large-scale signaling networks through nested effect models with intervention effects from microarray data. Bioinformatics, 24, 2650-2656.
8. Geistlinger, L. et al. (2011) From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems. Bioinformatics, 27, i366-i373.
9. Gentleman, R. et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol., 5, R80.
10. Johannes, M. et al. (2010) Integration of pathway knowledge into a reweighted recursive feature elimination approach for risk stratification of cancer patients. Bioinformatics, 26, 2136-2144.
11. Nishimura, D. (2001) BioCarta. Biotech. Software Internet Rep., 2, 117-120.
12. Schaefer, C.F. et al. (2009) PID: the Pathway Interaction Database. Nucleic Acids Res., 37, D674-D679.
13. Zhang, J.D. and Wiemann, S. (2009) KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor. Bioinformatics, 25, 1470-1471.