ChIPsim-package         Simulation of ChIP-seq experiments
bindDens2readDens       Convert a feature density into a read density
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
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
makeFeatures            Generating a list of genomic 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
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
