Man pages for bowang-lab/simATAC
This package is a single-cell ATAC-seq simulator
| getBin | Get the name of the input region from bed file in the format... |
| getBinNames | Set bin names based on the species variable of the... |
| getCountFromh5 | Extract count matrix from h5 file |
| getCountFromSCE | Return a sparse count matrix from a SingleCellExperiment... |
| getParameters | Get simATACCount parameters |
| newsimATACCount | newsimATACCount |
| setDefautParameters | Calculate the polynomial coefficients from an existing... |
| setParameters | Set parameters |
| simATACCompare | Compare the main parameters of simATAC's simulated bin by... |
| simATACCount | The simATACCount class |
| simATACEstBinMean | Estimate bin coverage mean |
| simATACEstimate | Estimate simATAC simulation parameters |
| simATACEstLibSize | Estimate library size parameters |
| simATACEstNonZeroPro | Estimate bins' non-zero cell proportion |
| simATACGenerate | Estimate and simulate simATAC simulation parameters |
| simATACget | Get a simATACCount parameter |
| simATACgetBinary | Convert raw bin by cell matrix in an SingleCellExperiment... |
| simATACgetFeatureByCell | Convert raw bin by cell matrix in an SingleCellExperiment... |
| simATACgetPeakByCell | Convert raw bin by cell matrix in an SingleCellExperiment... |
| simATACSimBinMean | Simulate bin means from estimated polynomial coefficients... |
| simATACSimLibSize | Simulate library sizes by sampling from a bimodal Gaussian... |
| simATACSimTrueCount | Adjust the simulated library sizes and bin means to generate... |
| simATACSimulate | simATAC simulation |
| simATACSimZeroEntry | Simulate zero and non-zero entries of simATAC simulation... |
| simBinMeans | Simulate a bin's mean from its non-zero cell proportion from... |
