Format

Send to

Choose Destination
Bioinformatics. 2014 Nov 1;30(21):3139-41. doi: 10.1093/bioinformatics/btu501. Epub 2014 Jul 28.

NetPathMiner: R/Bioconductor package for network path mining through gene expression.

Author information

1
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan and Department of Computing and Information Systems, The University of Melbourne, Victoria, Australia.
2
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan and Department of Computing and Information Systems, The University of Melbourne, Victoria, Australia Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan and Department of Computing and Information Systems, The University of Melbourne, Victoria, Australia.

Abstract

NetPathMiner is a general framework for mining, from genome-scale networks, paths that are related to specific experimental conditions. NetPathMiner interfaces with various input formats including KGML, SBML and BioPAX files and allows for manipulation of networks in three different forms: metabolic, reaction and gene representations. NetPathMiner ranks the obtained paths and applies Markov model-based clustering and classification methods to the ranked paths for easy interpretation. NetPathMiner also provides static and interactive visualizations of networks and paths to aid manual investigation.

AVAILABILITY:

The package is available through Bioconductor and from Github at http://github.com/ahmohamed/NetPathMiner.

PMID:
25075120
PMCID:
PMC4609018
DOI:
10.1093/bioinformatics/btu501
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center