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| ChIPsim-package | Simulation of ChIP-seq experiments |
| bindDens2readDens | Convert a feature density into a read density |
| ChIPsim | Simulation of ChIP-seq experiments |
| decodeQuality | Conversion between numerical and ASCII representation of read qualities |
| defaultControl | Default parameters for simChIP |
| defaultErrorProb | Replacement probabilities for sequencing errors |
| defaultFunctions | Default functions for simChIP |
| defaultGenerator | Defaults for Feature Generator |
| defaultInit | Defaults for Feature Generator |
| defaultLastFeat | Defaults for Feature Generator |
| defaultTransition | Defaults for Feature Generator |
| encodeQuality | Conversion between numerical and ASCII representation of read qualities |
| extractQuality | Obtain read qualities from a Fastq file or ShortReadQ object |
| feat2dens | Convert a list of features into a feature density |
| featureDensity | Computing density for a given feature |
| featureDensity.FuzzyFeature | Computing density for a given feature |
| featureDensity.NFRFeature | Computing density for a given feature |
| featureDensity.ReversePhasedFeature | Computing density for a given feature |
| featureDensity.StableFeature | Computing density for a given feature |
| featureDensity.StablePhasedFeature | Computing density for a given feature |
| fuzzyFeature | Generating Features |
| makeFeatures | Generating a list of genomic features |
| nfrFeature | Generating Features |
| phasedFeature | Generating Features |
| placeFeatures | Generating and reconciling a feature sequence |
| pos2fastq | Convert read positions to fastq records |
| readError | Introduce errors into read sequence based on quality scores |
| readQualitySample | Sample read qualities from a list |
| readSequence | Convert read position into read sequence |
| reconcileFeatures | Post-processing of simulated features |
| reconcileFeatures.default | Post-processing of simulated features |
| reconcileFeatures.NucleosomePosition | Post-processing of simulated features |
| reconcileFeatures.SimulatedExperiment | Post-processing of simulated features |
| sampleReads | Sampling sequence read positions from a read density. |
| simChIP | Simulate ChIP-seq experiments |
| simpleNames | Generate unique read names |
| stableFeature | Generating Features |
| writeFASTQ | Write read sequences and qualities to a FASTQ formatted file |
| writeReads | Create fastq file from read positions |