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SubpathwayMiner

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An R-based software package for flexible pathway identification. SubpathwayMiner facilitates sub-pathway identification of metabolic pathways by using pathway structure information. Additionally, SubpathwayMiner also provides more flexibility in annotating gene sets and identifying the involved pathways (entire pathways and sub-pathways): (i) SubpathwayMiner is able to provide the most up-to-date pathway analysis results for users; (ii) SubpathwayMiner supports multiple species (approximately 100 eukaryotes, 714 bacteria and 52 Archaea) and different gene identifiers (Entrez Gene IDs, NCBI-gi IDs, UniProt IDs, PDB IDs, etc.) in the KEGG GENE database; (iii) the system is quite efficient in cooperating with other R-based tools in biology.

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SubpathwayMiner versioning

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SubpathwayMiner classification

SubpathwayMiner specifications

Software type:
Package/Module
Restrictions to use:
None
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Interface:
Command line interface
Input data:
SubpathwayMiner supports three types of inputting data: gene list, compound list, gene and compound list.
Programming languages:
R
Version:
3.1
Source code URL:
https://cran.r-project.org/src/contrib/Archive/SubpathwayMiner/

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SubpathwayMiner forum

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Participate in the forum to get support for using tools. Ask questions about technical specifications.

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SubpathwayMiner classification

SubpathwayMiner specifications

Interface:
Web user interface
Input data:
SubpathwayMiner supports three types of inputting data: gene list, compound list, gene and compound list.
Computer skills:
Basic
Maintained:
Yes
Restrictions to use:
None
Programming languages:
R
Stability:
Stable

SubpathwayMiner support

Documentation

Maintainer

  • Xia Li <>
  • Xia Li <>

Credits

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Publications

Institution(s)

College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin, China; Princess Margaret Hospital in University Health Network, Toronto, ON, Canada

Funding source(s)

The National Natural Science Foundation of China (grant nos. 30871394, 30370798 and 30571034), the National High Tech Development Project of China, the 863 Program (grant nos. 2007AA02Z329), the National Basic Research Program of China, the 973 Program (grant nos. 2008CB517302) and the National Science Foundation of Heilongjiang Province (grant nos. ZJG0501, 1055HG009, GB03C602-4, and BMFH060044)

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