Tag: Biological Pathways

pathClass 0.9.4 – Classification using Biological Pathways as prior knowledge

pathClass 0.9.4

:: DESCRIPTION

pathClass is a collection of classification methods that use information about feature connectivity in a biological network as an additional source of information. This additional knowledge is incorporated into the classification a priori. Several authors have shown that this approach significantly increases the classification performance.

::DEVELOPER

pathClass team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 pathClass

:: MORE INFORMATION

Citation

Bioinformatics. 2011 May 15;27(10):1442-3. doi: 10.1093/bioinformatics/btr157. Epub 2011 Mar 30.
pathClass: an R-package for integration of pathway knowledge into support vector machines for biomarker discovery.
Johannes M1, Fröhlich H, Sültmann H, Beissbarth T.

PNmerger 1.0 – Merge Biological Pathways and Protein Interaction Networks

PNmerger 1.0

:: DESCRIPTION

PNmerger (biological Pathway and protein Netwrok merge) is a java based plug-in for the widely used open-source Cytoscape molecular interaction viewer.

::DEVELOPER

Li Dong

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / MacOs
  • Java
  • Cytoscape

:: DOWNLOAD

  PNmerger

:: MORE INFORMATION

Citation

Sun, H.; Li, D.; Wang, J.; Liu, Z.; Zhu, Y.; Xie, H.; He, F.,
Nmerger: a Cytoscape plugin to merge biological pathways and protein interaction networks.
Progress in Biochemistry and Biophysics. Accepted.

PathVisio 3.3.0 – a tool to Edit and Analyze Biological Pathways

PathVisio 3.3.0

:: DESCRIPTION

PathVisio is a free open-source biological pathway analysis software that allows you to draw, edit and analyze biological pathways.

::DEVELOPER

PathVisio team

:: SCREENSHOTS

PathVisio

::REQUIREMENTS

  • Linux / Solaris / MacOS X
  • Java

:: DOWNLOAD

 PathVisio

:: MORE INFORMATION

Citation

PathVisio 3: an extendable pathway analysis toolbox.
Kutmon M, van Iersel MP, Bohler A, Kelder T, Nunes N, Pico AR, Evelo CT.
PLoS Comput Biol. 2015 Feb 23;11(2):e1004085. doi: 10.1371/journal.pcbi.1004085.

Presenting and exploring biological pathways with PathVisio
Iersel, Martijn P van, Thomas Kelder, Alexander R Pico, Kristina Hanspers, Susan Coort, Bruce R Conklin, and Chris Evelo
BMC Bioinformatics 2008, 9:399