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TIGRESS specifications

Information


Unique identifier OMICS_01687
Name TIGRESS
Alternative name Trustful Inference of Gene REgulation using Stability Selection
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Jean-Philippe Vert <>

Publication for Trustful Inference of Gene REgulation using Stability Selection

TIGRESS in publications

 (5)
PMCID: 5360040
PMID: 28344638
DOI: 10.1186/s13015-017-0100-5

[…] to a 1000-variable in silico data set illustrates the viability of reverse engineering of genome-scale biological networks. results from the gpu method were compared with a widely used method called tigress  []. tigress combines least angle regression (lars)  [] with stability selection  [, ] and was ranked among the top five network inference methods in the dream5 gene reconstruction challenge   […]

PMCID: 5260093
PMID: 28155657
DOI: 10.1186/s12864-016-3317-7

[…] []), one bayesian network based method (sign-bn []), two random forest based method (genie3 [] with two different parameter settings, see table  for the details), two regression based method (tigress [] with two different parameter settings, see table  for the details), and one method with both of ordinary differential equation based recursive optimization and mutual information (narromi […]

PMCID: 5001240
PMID: 27556418
DOI: 10.1186/s12864-016-2791-2

[…] regression coefficients for these variables; 2. the model suffers from severe overfitting which necessitates the use of variable selection strategies. a few successful methods have been reported. tigress [] treats grn inference as a sparse regression problem and introduce least angle regression in conjunction with stability selection to choose target genes for each tf. genie3 [] performs […]

PMCID: 4333722
PMID: 25533953
DOI: 10.1038/nature14099

[…] considered in the inference. the unsupervised regulatory interaction network was constructed using the consensus from four different gene regulatory network inference methods, genie3, inferelator, tigress and anoverence. the data used were the same as the supervised tieria network. the default parameters were used in all methods and a rank-based method was used to build the consensus network […]

PMCID: 3900469
PMID: 24428926
DOI: 10.1186/1752-0509-8-5

[…] reverse engineering methods. to be specific, in this set of experiments, the dream4 multifactorial network 1 with 100 nodes was used, and two well-known inference algorithms (genie3 [] and tigress []) were chosen for comparison. our approach was performed with two fitness functions: (a) the mse function, and (b), the fitness function described in part c of the additional file . […]


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TIGRESS institution(s)
Centre for Computational Biology, Mines ParisTech, Fontainebleau, France

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