:: DESCRIPTION
GeneNT is a R package to estimate co-expression gene networks
::DEVELOPER
Dongxiao Zhu, Ph.D
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Network constrained clustering for gene microarray data.
Zhu D, Hero AO, Cheng H, Khanna R, Swaroop A.
Bioinformatics. 2005 Nov 1;21(21):4014-20.
:: DESCRIPTION
BIANA (Biologic Interactions and Network Analysis) is a biological database integration and network management framework written in Python. It uses a high level abstraction schema to define databases providing any kind of biological information (both individual entries and their relationships).
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Biana: a software framework for compiling biological interactions and analyzing networks.
Garcia-Garcia J, Guney E, Aragues R, Planas-Iglesias J, Oliva B.
BMC Bioinformatics. 2010 Jan 27;11:56.
:: DESCRIPTION
EnrichNet is a network-based enrichment analysis method to identify functional associations between user-defined gene or protein sets and cellular pathways. The datasets are mapped onto a protein interaction network (or other user-defined molecular network) and their pairwise associations are assessed by computing a graph-based statistic, i.e. distances between the network nodes are mapped against a background model. In contrast to the classical overlap-based enrichment analysis, associations can also be identified for non-overlapping gene/protein sets and the user can investigate them in detail by visualizing corresponding sub-graphs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
Bioinformatics. 2012 Sep 15;28(18):i451-i457. doi: 10.1093/bioinformatics/bts389.
EnrichNet: network-based gene set enrichment analysis.
Glaab E, Baudot A, Krasnogor N, Schneider R, Valencia A.
:: DESCRIPTION
ReMoDiscovery is an intuitive algorithm to correlate regulatory programs with regulators and corresponding motifs to a set of co-expressed genes. It exploits in a concurrent way three independent data sources: ChIP-chip data, motif information and gene expression profiles.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: MORE INFORMATION
Citation
Genome Biol. 2006;7(5):R37. Epub 2006 May 5.
Inferring transcriptional modules from ChIP-chip, motif and microarray data.
Lemmens K, Dhollander T, De Bie T, Monsieurs P, Engelen K, Smets B, Winderickx J, De Moor B, Marchal K.
:: DESCRIPTION
CytoHiC is a plugin for the Cytoscape platform which allows users to view and visually compare spatial maps of genomic landmarks, based on normalized Hi-C data.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
CytoHiC: a cytoscape plugin for visual comparison of Hi-C networks.
Yoli Shavit; Pietro Lio’.
Bioinformatics 2013; doi: 10.1093/bioinformatics/btt120
:: DESCRIPTION
CFNet combines a novel rotation equivariant convolution scheme, called conic convolution, and the DFT to aid networks in learning rotation-invariant tasks. This network has been especially designed to improve performance of CNNs on automated computational tasks related to microscopy image analysis.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2019 Jul 15;35(14):i530-i537. doi: 10.1093/bioinformatics/btz353.
Rotation equivariant and invariant neural networks for microscopy image analysis.
Chidester B, Zhou T, Do MN, Ma J.
:: DESCRIPTION
WebPropagate is a web-server that implements variants of network propagation on up-to-date PPI networks. Starting from a seed set of proteins that are known to be associated with a process of interest, WebPropagate outputs additional candidate proteins that are significantly associated with the seed set.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
WebPropagate: A Web Server for Network Propagation.
Biran H, Almozlino T, Kupiec M, Sharan R.
J Mol Biol. 2018 Jul 20;430(15):2231-2236. doi: 10.1016/j.jmb.2018.02.025.
:: DESCRIPTION
NCIS (network-assisted co-clustering for the identification of cancer subtypes) combines molecular interaction network into co-clustering.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2014 Feb 4;15:37. doi: 10.1186/1471-2105-15-37.
A network-assisted co-clustering algorithm to discover cancer subtypes based on gene expression.
Liu Y, Gu Q, Hou JP, Han J, Ma J
:: DESCRIPTION
PhosNetConstruct is a tool to predict novel phosphorylation networks based on the preference of certain kinase families to phosphorylate specific functional protein families (domains). It identifies the potentially phosphorylated proteins from a given set of proteins and predicts target kinases which in turn would phosphorylate these identified phosphoproteins based on their domain compositions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Jun 15;30(12):1730-8. doi: 10.1093/bioinformatics/btu112. Epub 2014 Feb 25.
Deciphering kinase-substrate relationships by analysis of domain-specific phosphorylation network.
Damle NP, Mohanty D.
:: DESCRIPTION
PRINCE (PRIoritizatioN and Complex Elucidation) is a method for prioritizing disease associated genes.PRINCIPLE (PRINCe ImPLEmentation) is a client-server implementation of PRINCE
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Dec 1;27(23):3325-6. doi: 10.1093/bioinformatics/btr584. Epub 2011 Oct 20.
PRINCIPLE: a tool for associating genes with diseases via network propagation.
Gottlieb A1, Magger O, Berman I, Ruppin E, Sharan R.