• BGRMI

  • Referenced in 2 articles [sw29320]
  • BGRMI: A method for inferring gene regulatory networks from time-course gene expression data ... application in breast cancer research. Reconstructing gene regulatory networks (GRNs) from gene expression data ... fast but less accurate. We propose Bayesian Gene Regulation Model Inference (BGRMI), a model-based ... regulatory networks of proliferating and differentiating breast cancer (BC) cells from time-course gene expression...
  • ARACNe-AP

  • Referenced in 3 articles [sw34267]
  • mutual information. The accurate reconstruction of gene regulatory networks from large scale molecular profile datasets ... resources to build complex regulatory networks from hundreds of gene expression profiles. Availability and Implementation...
  • GENeVis

  • Referenced in 2 articles [sw06743]
  • Interactive visualization of gene regulatory networks with associated gene expression time series data We present ... expression time series data in a gene regulatory network context. This is a network ... regulate the expression of their respective target genes. The networks are represented as graphs...
  • Ginsim

  • Referenced in 29 articles [sw09090]
  • model analysis of the inter-cellular regulatory network activating Notch at the dorsal–ventral boundary ... focus on the cross-regulations between five genes (within and between two cells), which implements...
  • GeNGe

  • Referenced in 2 articles [sw29326]
  • GeNGe: systematic generation of gene regulatory networks. Summary: The analysis of gene regulatory networks (GRNs ... have developed the web application GeNGe (GEne Network GEnerator), a controlled framework for the automatic...
  • REVEAL

  • Referenced in 28 articles [sw36999]
  • inference of genetic network architectures. Given the immanent gene expression mapping covering whole genomes during ... principle, to completely infer a complex regulatory network architecture from input/output patterns of its variables ... networks. Trajectories, or state transition tables of Boolean nets, resemble time series of gene expression...
  • BNArray

  • Referenced in 2 articles [sw30810]
  • BNArray: An R package for constructing gene regulatory networks from microarray data by using Bayesian ... facilitates the construction of gene regulatory networks from DNA microarray data by using Bayesian network...
  • NetBenchmark

  • Referenced in 2 articles [sw29311]
  • bioconductor package for reproducible benchmarks of gene regulatory network inference. Background: In the last decade ... great number of methods for reconstructing gene regulatory networks from expression data have been proposed...
  • KELLER

  • Referenced in 3 articles [sw22600]
  • time-varying interactions between genes. MOTIVATION: Gene regulatory networks underlying temporal processes, such ... capture the temporal evolution of the regulatory networks. These methods will be an enabling first ... studying the driving forces underlying the dynamic gene regulation circuitry and predicting the future network...
  • VirtualLeaf

  • Referenced in 4 articles [sw28766]
  • insight into the roles of gene products in regulatory networks, the conditions of gene expression...
  • multistatepdscontrol

  • Referenced in 2 articles [sw31987]
  • modify intracellular networks, such as gene regulatory networks or signaling networks, in order for cells...
  • maigesPack

  • Referenced in 1 article [sw25800]
  • statistical method for measuring activation of gene regulatory networks. Motivation: Gene expression data analysis ... model for the activation measuring of gene regulatory networks, instead of the traditional gene ... statistical procedure for testing hypothesis regarding gene regulatory network activation. The real probability distribution ... hypothetical network and the activation measuring of two KEGG networks, both based on gene expression...
  • expansion-network

  • Referenced in 1 article [sw34481]
  • regulomics/expansion-network: Automated inference of gene regulatory networks using explicit regulatory modules. Gene regulatory networks ... factors to distinct regulatory regions. Recent gene regulatory network models use binding measurements; but usually ... only to define gene-to-gene interactions, ignoring regulatory module structure. Moreover, current huge amount ... method to specify possible regulatory connections in a given Boolean network, based on transcription factor...
  • SCENIC

  • Referenced in 2 articles [sw29313]
  • SCENIC, a computational method for simultaneous gene regulatory network reconstruction and cell-state identification from...
  • optPBN

  • Referenced in 2 articles [sw32145]
  • optPBN: An optimisation toolbox for probabilistic boolean networks. SUMMARY: The optPBN toolbox provides a simple ... studies such as the inference of gene regulatory networks or the identification of the interaction...
  • SELANSI

  • Referenced in 2 articles [sw28254]
  • simulation of stochastic multidimensional Gene Regulatory Networks (GRNs). SELANSI exploits intrinsic structural properties of GRNs...
  • bc3net

  • Referenced in 1 article [sw17708]
  • package bc3net: Gene Regulatory Network Inference with Bc3net. Implementation of the BC3NET algorithm for gene ... regulatory network inference (de Matos Simoes and Frank Emmert-Streib, Bagging Statistical Network Inference from ... Large-Scale Gene Expression Data, PLoS ONE 7(3): e33624...
  • PyPanda

  • Referenced in 1 article [sw14828]
  • Regulatory Network Reconstruction. PANDA (Passing Attributes between Networks for Data Assimilation) is a gene regulatory...
  • RoVerGeNe

  • Referenced in 13 articles [sw10954]
  • Gene Networks. Rovergene is a tool for the analysis of genetic regulatory networks under parameter ... uncertainty. Genetic regulatory networks are described by a class of piecewise multiaffine differential equation models ... robustness of dynamical properties of gene networks with respect to parameter variations...
  • graphsim

  • Referenced in 1 article [sw33833]
  • Data from ’igraph’ Networks. Functions to develop simulated continuous data (e.g., gene expression) from ... versatile statistical framework to simulate correlated gene expression data from biological pathways, by sampling from ... methods to infer biological pathways and gene regulatory networks from gene expression data...