Aims at validating image analysis and spot quantification and simulate TIF-images of the visualized spots. The SIMAGE web site consists of three parts: (i) a start page where the user may upload parameters for a simulation; (ii) a web-page where the user specifies a number of parameters, after which (iii) the results, namely simulated data (see below), are presented. This software also simulates dual-dye DNA microarray data.
Allows to generate two conditions biological synthetic microarray dataset with known characteristics. madsim is a flexible microarray data simulation model where user provides a subset of parameters. A detailed description of these parameters is available in the reference given below. The generated data have similar behavior as those obtained with current microarray platforms. Available default parameters settings can also be modified.
An R-package to simulate gene expression and DNA methylation data. The R-package quantroSim is the supporting data simulation package for the quantro R/Bioconductor package which can be used to simulate data from the epigenome including gene expression (microarrays, but will be extended to include RNA-Seq) and DNA methylation (microarrays).
Allows identification of molecular subtypes of disease. InterSIM is a program that focuses on three types of data: (1) DNA methylation, (2) mRNAgene expression, and (3) protein expression. These data are come from three datasets based on the ovarian cancer study. Moreover, this tool can generate multiple types of omics data.
Simulates time course transcriptional data. CancerInSilico extends the off-lattice, cell-center Drasdo and Höhme Monte Carlo mathematical model to simulate treatment with growth factor receptor inhibitors, cellular-level variation in model parameters, and multiple cell types. The software includes extensions to simulate single cell RNA-seq data. It was used to mirror real in vitro cancer cells with and without cetuximab treatment and in vivo growth of a patient derived xenograft tumor model.