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Fig. 1 | Genome Biology

Fig. 1

From: simATAC: a single-cell ATAC-seq simulation framework

Fig. 1

The simATAC simulation framework. The red circles represent values directly extracted from the user-input bin-by-cell matrix, the white squares represent estimated parameters, and the brown circles represent the simulated values. simATAC initially estimates the library sizes, the non-zero cell proportions, and the bin means from the input cell group (including cells having similar biological characteristics). simATAC generates the library sizes with a Gaussian mixture distribution, the zero and non-zero status with a Bernoulli distribution, and the bin means with a polynomial regression model linking to the non-zero cell proportion. The synthetic counts are sampled from a Poisson distribution whose mean is a factor of the cell library size adjusted by the bin mean. simATAC offers optional sparsity adjustment factor γ and noise parameters to adjust the sparsity and noise level of the synthetic counts generated from the Poisson distribution. The simATAC framework simulates synthetic scATAC-seq data using the default values for all the parameters if no user-input real data or parameters are given

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