NetDecoder – Network-based Platform to Decode Context-Specific Biological Networks and Gene Activities

NetDecoder

:: DESCRIPTION

NetDecoder is a novel network biology-based computational platform designed to integrate transcriptomes, interactomes and gene ontologies to identify phenotype-specific subnetworks.

::DEVELOPER

Hu Li Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / Max OS X
JAVA

:: DOWNLOAD

NetDecoder

:: MORE INFORMATION

Citation:

NetDecoder: a network biology platform that decodes context-specific biological networks and gene activities.
da Rocha EL, Ung CY, McGehee CD, Correia C, Li H.
Nucleic Acids Res. 2016 Mar 14. pii: gkw166.

CoGAPS 3.10.0 – Coordinated Gene Activity in Pattern Sets

CoGAPS 3.10.0

:: DESCRIPTION

CoGAPS identifies overlapping coregulation between genes and improves inference of biological process activity. CoGAPS achieves this improvement by combining an MCMC matrix factorization algorithm (GAPS) with a threshold-independent statistic inferring activity on gene sets.

::DEVELOPER

Division of Biostatistics and Bioinformatics – Johns Hopkins University Oncology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Windows/MacOsX
R
BioConductor

:: DOWNLOAD

CoGAPS

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 Nov 1;26(21):2792-3. doi: 10.1093/bioinformatics/btq503. Epub 2010 Sep 1.
CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data.
Fertig EJ1, Ding J, Favorov AV, Parmigiani G, Ochs MF.