Man pages for ChIPsim
Simulation of ChIP-seq experiments

bindDens2readDensConvert a feature density into a read density
ChIPsim-packageSimulation of ChIP-seq experiments
decodeQualityConversion between numerical and ASCII representation of read...
defaultControlDefault parameters for simChIP
defaultErrorProbReplacement probabilities for sequencing errors
defaultFunctionsDefault functions for simChIP
defaultGeneratorDefaults for Feature Generator
distDensComputing densities for nucleosome positioning simulation
extractQualityObtain read qualities from a Fastq file or ShortReadQ object
feat2densConvert a list of features into a feature density
featureDensityComputing density for a given feature
internalInternal and undocumented functions
joinRegionCombining two feature densities
makeFeaturesGenerating a list of genomic features
placeFeaturesGenerating and reconciling a feature sequence
pos2fastqConvert read positions to fastq records
readErrorIntroduce errors into read sequence based on quality scores
readQualitySampleSample read qualities from a list
readSequenceConvert read position into read sequence
reconcileFeaturesPost-processing of simulated features
sampleReadsSampling sequence read positions from a read density.
simChIPSimulate ChIP-seq experiments
simpleNamesGenerate unique read names
stableFeatureGenerating Features
writeFASTQWrite read sequences and qualities to a FASTQ formatted file
writeReadsCreate fastq file from read positions
ChIPsim documentation built on Oct. 31, 2019, 2:09 a.m.