:: DESCRIPTION
grnl1 is a software of gene regulatory network modeling using L1 regularized graphical models
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2012;7(5):e35762. doi: 10.1371/journal.pone.0035762. Epub 2012 May 7.
Learning transcriptional regulatory relationships using sparse graphical models.
Zhang X1, Cheng W, Listgarten J, Kadie C, Huang S, Wang W, Heckerman D.
:: DESCRIPTION
REDUCE (REDuction of UnCertain Edges) is an algorithm for finding the optimal gene KO experiment for inferring directed graphs (digraphs) of gene regulatory network (GRN).
:: DEVELOPER
Chemical and Biological Systems Engineering Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Optimal design of gene knock-out experiments for gene regulatory network inference.
Ud-Dean SM, Gunawan R.
Bioinformatics. 2015 Nov 14. pii: btv672
:: DESCRIPTION
CN (Consensus Network) is a network inference method based on the SORDER algorithm and a suitable interval threshold for Conditional Mutual Information (CMI) tests
::DEVELOPER
School of Biological Sciences, Iran
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
CN: a consensus algorithm for inferring gene regulatory networks using the SORDER algorithm and conditional mutual information test.
Aghdam R, Ganjali M, Zhang X, Eslahchi C.
Mol Biosyst. 2015 Mar;11(3):942-9. doi: 10.1039/c4mb00413b
:: DESCRIPTION
IPCA-CMI is an algorithm for inferring gene regulatory networks based on a combination of PCA-CMI and MIT score.
::DEVELOPER
School of Biological Sciences, Iran
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2014 Apr 11;9(4):e92600. doi: 10.1371/journal.pone.0092600. eCollection 2014.
IPCA-CMI: an algorithm for inferring gene regulatory networks based on a combination of PCA-CMI and MIT score.
Aghdam R1, Ganjali M1, Eslahchi C
:: DESCRIPTION
LDGM estimates differential network between two tissue types directly without inferring the network for individual tissues.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2016 Sep 30;44(17):e140. doi: 10.1093/nar/gkw581.
Identifying gene regulatory network rewiring using latent differential graphical models.
Tian D, Gu Q, Ma J.
:: DESCRIPTION
ModEnt is a computational tool that reconstructs gene regulatory networks from high throughput experimental data.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Karlebach, G. and Shamir, R.,
Constructing logical models of gene regulatory networks by integrating transcription factor-DNA interactions with expression data: an entropy based approach.
Journal of Computational Biology.2012 Jan;19(1):30-41.
:: DESCRIPTION
GPODE (GP4GRN) is a software of learning the structure of gene regulatory networks using non-parametric molecular kinetics. A set of Matlab functions that implement our gene regulatory network inference method. The method can use time-series and steady state gene expression (and protein) measurements and makes Bayesian inference for the network structure using Gaussian process based non-parametric molecular kinetics
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2009 Nov 15;25(22):2937-44. Epub 2009 Aug 25.
Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics.
Aijö T, Lähdesmäki H.
:: DESCRIPTION
geneDBN is a software to build gene regulatory networks based on DBN (dynamic Bayesian network).
::DEVELOPER
Complex Computation Laboratory ,Iowa State University
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
Registration First ; geneDBN
:: MORE INFORMATION
Copyright (C) 2007 Song Li and Hui-Hsien Chou.Bug report and suggestions are welcome and can be sent to geneDBN@www.complex.iastate.edu.
:: DESCRIPTION
SpotXplore is a plug-in for Cytoscape which enhances the visual analysis of gene expression obtained by, e.g., microarrays or the newer RNA-seq techniques in various ways. It enables visualization of multiple conditions or time series by glyphs that encode both expression value and statistical confidence.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
M. A. Westenberg, J. B. T. M. Roerdink, O. P. Kuipers, S. A. F. T. van Hijum.
SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks.
Bioinformatics, 26(22):2922-2923, 2010.
:: DESCRIPTION
GRNInfer aims to derive the most consistent network structure with respect to Multiple Microarray Datasets, by exploiting available information from a variety of experiments. Specifically, inferring gene network is formulated as an optimization problem with minimization of L1 norm for the objective function, which involves both forced matching and sparse terms. An efficient algorithm is developed to solve such a large-scale linear programming in an iterative manner. With such a procedure, a consistent and sparse structure that is also considered to be biologically plausible, can be expected to be derived.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Yong Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, and Luonan Chen.
Inferring gene regulatory networks from multiple microarray datasets.
Bioinformatics, Vol. 22, No. 19, pp. 2413-2420, 2006.