Inferelator protocols

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Inferelator specifications

Information


Unique identifier OMICS_01684
Name Inferelator
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Inferelator

Inferelator in pipeline

2013
PMCID: 3919619
PMID: 24185701
DOI: 10.1093/nar/gkt938

[…] into the large-scale network to improve the overall predictive power., this article combines both computational and biological methods. the computational methods used in this research, cmonkey and inferelator (,), were originally developed to study h. salinarum (). we adapted these tools to eukaryotic s. cerevisiae and included a number of changes detailed below. unless otherwise noted, […]


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Inferelator in publications

 (35)
PMCID: 5453602
PMID: 28520713
DOI: 10.1371/journal.pcbi.1005489

[…] under what environmental conditions those factors are relevant. it uses the biclustering algorithm, cmonkey [] to find conditionally co-regulated genes from heterogeneous genome-wide datasets, and inferelator [] to use the mrna expression levels of tfs or other regulators to predict the expression level of a target gene with linear regression model. egrin construction techniques […]

PMCID: 5371734
PMID: 28320772
DOI: 10.15252/msb.20167058

[…] n be explored at http://networks.systemsbiology.net/syntrophy)., environment and gene regulatory influence network (egrin) model was constructed as described in . this model includes both cmonkey and inferelator algorithm input data and results together with different filtering parameters as defined below., number of modules filtered for residual ≤ 0.5., number of motifs filtered for e‐value <  […]

PMCID: 5309336
PMID: 28217746
DOI: 10.1128/mSystems.00142-16

[…] phatr3 gene ids with an in-house phatr2-to-phatr3 gene id mapping table. the cmonkey2 algorithm was run for 2,000 iterations and generated 121 biclusters with a mean of 20 genes per cluster., the inferelator algorithm was used to infer the regulatory influences of 196 tfs influencing the expression of the coregulated modules discovered by cmonkey2 ()., the python tool goatools version 0.5.9 […]

PMCID: 5293552
PMID: 28166542
DOI: 10.1371/journal.pone.0171240

[…] and slab” prior [], which at the same time enforces sparsity of the network. the spike and slab prior is known to yield less biased estimates than lasso-type l1 penalties, as e.g. employed in the “inferelator” []., to ease the representation of our model, we first assume we have time-series data. the case of steady state data will be explained later. let y = {y1,y2,…,yn} be the molecules […]

PMCID: 5241943
PMID: 28133490
DOI: 10.1155/2017/8307530

[…] method still has the highest average auroc. the prediction performances on the dream3 10 gene networks are summarized in . we also compared our method with another additive model based on ode [] and inferelator 1.0 []. for ecoli 1, ecoli 2, yeast 2, and yeast 3, the 3 additive models perform better than the linear model; for yeast 1, although bl performs much better than bgl, the bgl_prior still […]


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Inferelator institution(s)
Computational Biology Program, New York University Sackler School of Medicine, New York, NY, USA

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