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 |