Rintact: enabling computational analysis of molecular interaction data from the IntAct repository.
BACKGROUND
The IntAct repository is one of the largest and most widely used databases for the curation and storage of molecular interaction data. These datasets need to be analyzed by computational methods. Software packages in the statistical environment R provide powerful tools for conducting such analyses.


RESULTS
We introduce Rintact, a Bioconductor package that allows users to transform PSI-MI XML2.5 interaction data files from IntAct into R graph objects. On these, they can use methods from R and Bioconductor for a variety of tasks: determining cohesive subgraphs, computing summary statistics, fitting mathematical models to the data or rendering graphical layouts. Rintact provides a programmatic interface to the IntAct repository and allows the use of the analytic methods provided by R and Bioconductor.


BACKGROUND
Rintact is freely available at http://bioconductor.org
Chiang
Tony
T
EBI-EMBL, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Li
Nianhua
N
Orchard
Sandra
S
Kerrien
Samuel
S
Hermjakob
Henning
H
Gentleman
Robert
R
Huber
Wolfgang
W
D003196:Computer Graphics; D003628:Database Management Systems; D030562:Databases, Protein; D016247:Information Storage and Retrieval / Q000379:methods*; D011381:Programming Languages; D025941:Protein Interaction Mapping / Q000379:methods*; D012984:Software; D014584:User-Computer Interface