| mosaics-package | MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq) |
| bdBin-method | Class "MosaicsPeak" |
| BinData-class | Class "BinData" |
| chrID-method | Class "BinData" |
| constructBins | Construct bin-level ChIP-sep data from an aligned read file |
| coord-method | Class "BinData" |
| empFDR-method | Class "MosaicsPeak" |
| estimates | Extract estimates of the fitted MOSAiCS model |
| estimates-method | Class "MosaicsHMM" |
| estimates-method | Extract estimates of the fitted MOSAiCS model |
| export | Export peak calling results to text files |
| export-method | Export peak calling results to text files |
| gcContent-method | Class "BinData" |
| generateWig | Construct wiggle files from an aligned ChIP-sep read file |
| input-method | Class "BinData" |
| mappability-method | Class "BinData" |
| mosaics | MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq) |
| mosaicsFit | Fit MOSAiCS model |
| MosaicsFit-class | Class "MosaicsFit" |
| mosaicsFit-method | Fit MOSAiCS model |
| mosaicsFitHMM | Fit MOSAiCS-HMM model |
| mosaicsFitHMM-method | Fit MOSAiCS-HMM model |
| MosaicsHMM-class | Class "MosaicsHMM" |
| mosaicsPeak | Call peaks using fitted MOSAiCS model |
| MosaicsPeak-class | Class "MosaicsPeak" |
| mosaicsPeak-method | Call peaks using fitted MOSAiCS model |
| mosaicsPeakHMM | Call broad peaks using fitted MOSAiCS-HMM model |
| mosaicsPeakHMM-method | Call broad peaks using fitted MOSAiCS-HMM model |
| mosaicsRunAll | Analyze ChIP-seq data using the MOSAiCS framework |
| plot-method | Class "BinData" |
| plot-method | Class "MosaicsFit" |
| plot-method | Class "MosaicsHMM" |
| print-method | Class "BinData" |
| print-method | Class "MosaicsFit" |
| print-method | Class "MosaicsHMM" |
| print-method | Class "MosaicsPeak" |
| readBins | Import bin-level ChIP-sep data |
| show-method | Class "BinData" |
| show-method | Class "MosaicsFit" |
| show-method | Class "MosaicsHMM" |
| show-method | Class "MosaicsPeak" |
| tagCount-method | Class "BinData" |