• boost

  • Referenced in 40 articles [sw35655]
  • boost: BagBoosting for tumor classification with gene expression data. Motivation: Microarray experiments are expected ... bagging and boosting on real and simulated gene expression data. This quasi-guaranteed improvement ... algorithms, for benchmark studies and for the simulation of microarray data are available...
  • GeneRank

  • Referenced in 17 articles [sw27064]
  • from gene annotations (gene ontologies) or expression profile correlations. Using both simulated and real data ... algorithm offers an improved ranking of genes compared to pure expression change rankings. Conclusion...
  • GNA

  • Referenced in 25 articles [sw35974]
  • computer tool for the modeling and simulation of genetic regulatory networks ... combination with gene expression data. Genetic Network Analyzer consists of a simulator of qualitative models...
  • Ginsim

  • Referenced in 29 articles [sw09090]
  • border in the developing imaginal disc. Our simulations qualitatively reproduce the wild-type developmental pathway ... function mutations or ectopically induced gene expression...
  • SSS

  • Referenced in 33 articles [sw07794]
  • gene expression cancer genomics, comparisons with MCMC and other methods, and theoretical and simulation-based...
  • TABASCO

  • Referenced in 2 articles [sw20856]
  • expression simulator. TABASCO is a simulator created to address the problem of simulating gene expression ... system as it develops and thus makes simulation at such high resolution computationally feasible. Tabasco ... allow us to better understand bacteriophage gene expression. In general, Tabasco would be useful ... explicitly simulating hypotheses of protein-DNA interactions and their relation to gene expression (e.g., eukaryotic...
  • E-CELL

  • Referenced in 23 articles [sw07917]
  • silico. RESULTS: E-CELL, a modeling and simulation environment for biochemical and genetic processes ... interactions, protein-DNA interactions, regulation of gene expression and other features of cellular metabolism ... reaction rules. E-CELL simulates cell behavior by numerically integrating the differential equations described implicitly ... hypothetical cell with only 127 genes sufficient for transcription, translation, energy production and phospholipid synthesis...
  • SIMAGE

  • Referenced in 4 articles [sw10459]
  • SIMAGE: simulation of DNA-microarray gene expression data. Software overview: The SIMAGE web site ... user may upload parameters for a simulation; (ii) a web-page where the user specifies ... parameters, after which (iii) the results, namely simulated data (see below), are presented. Each ... SIMAGE for future simulations; (ii) the (differential) gene expressions, which are obtained after applying only...
  • sgnesR

  • Referenced in 1 article [sw29327]
  • sgnesR: an R package for simulating gene expression data from an underlying real gene network ... Expression Simulator in R) is an R package that provides an interface to simulate gene ... expression data from a given gene network using the stochastic simulation algorithm (SSA). The package ... present two network models to generate expression profiles. We also demonstrated the inference of networks...
  • PenPC

  • Referenced in 7 articles [sw25384]
  • illustrated by extensive simulations and applications on gene expression data of cancer patients, 𝖯𝖾𝗇𝖯𝖢...
  • graphsim

  • Referenced in 1 article [sw33833]
  • Networks. Functions to develop simulated continuous data (e.g., gene expression) from a sigma covariance matrix ... versatile statistical framework to simulate correlated gene expression data from biological pathways, by sampling from ... regulatory networks from gene expression data can be tested on simulated datasets using this framework ... considered as a confounding variable when simulating gene expression data to test the performance...
  • SimSeq

  • Referenced in 4 articles [sw34306]
  • control the proportion of genes simulated to be differentially expressed (DE) and can provide...
  • grndata

  • Referenced in 1 article [sw40326]
  • Synthetic Expression Data for Gene Regulatory Network Inference. Simulated expression data for five large Gene...
  • StochPy

  • Referenced in 8 articles [sw27252]
  • stochastic simulations. We illustrate the functionality of StochPy with stochastic models of gene expression, cell ... comprehensive software package for stochastic simulation of the molecular control networks of living cells...
  • DEMSIM

  • Referenced in 2 articles [sw33863]
  • discrete event based mechanistic simulation platform for gene expression and regulation dynamics...
  • APPLE

  • Referenced in 4 articles [sw13354]
  • well-known packages via simulation and analysis of two gene expression data sets...
  • STOCKS

  • Referenced in 13 articles [sw10438]
  • algorithm. STOCKS, software for the stochastic kinetic simulation of biochemical processes is presented. The program ... applicable to the study of prokaryotic gene expression. Features dedicated to the study of cellular ... simple cell division model. Taking expression of Escherichia coli beta-galactosidase as an example ... shown that the program is able to simulate systems composed of reactions varying in several...
  • BDgraph

  • Referenced in 12 articles [sw14815]
  • method on a broad range of simulated data. We then apply the method on large ... applications from human and mammary gland gene expression studies to show its empirical usefulness...
  • compHclust

  • Referenced in 3 articles [sw19128]
  • from these novel genes that are not as highly expressed. Simulation studies show that ... also define a concept called relative gene importance that can be used to identify...
  • Hy3S

  • Referenced in 5 articles [sw23355]
  • developing, integrating, and disseminating software that simulates a chemical or biochemical system as quickly ... regulated gene expression to produce useful behavior. By combining quantitatively predictive simulations and design algorithms...