Package: ChIPsim 1.66.0

Peter Humburg

ChIPsim: Simulation of ChIP-seq experiments

A general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments.

Authors:Peter Humburg

ChIPsim_1.66.0.tar.gz
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ChIPsim_1.66.0.tgz(r-4.6-any)ChIPsim_1.66.0.tgz(r-4.5-any)
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manual.pdf |manual.html✨
card.svg |card.png
ChIPsim/json (API)

# Install 'ChIPsim' in R:
install.packages('ChIPsim', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:ChIPsim-1.67.0(bioc 3.24)ChIPsim-1.66.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

infrastructurechipseq

4.00 score 5 scripts 1 mentions 40 exports 45 dependencies

Last updated from:324ae9cc67 (on RELEASE_3_23). Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR224
linux-devel-x86_64NOTE358
source / vignettesOK263
linux-release-x86_64NOTE314
macos-release-arm64NOTE245
macos-oldrel-arm64NOTE204
windows-develNOTE241
windows-releaseNOTE219
windows-oldrelNOTE225
wasm-releaseOK125

Exports:bindDens2readDensbindLocDensdecodeQualitydefaultControldefaultErrorProbdefaultFunctionsdefaultGeneratordefaultInitdefaultLastFeatdefaultTransitiondistDensencodeQualityextractQualityfeat2densfeatureDensityfragDensfuzzyFeatureindNucjoinRegionmakeFeaturesnfrFeaturenoNucphasedFeaturephaseNucplaceFeaturespos2fastqreadErrorreadQualitySamplereadSequencereconcileFeaturessampleFromFilesampleReadssimChIPsimpleNamessolexaNamesstableDensstableFeaturewriteFASTQwriteIlluminawriteReads

Dependencies:abindBHBiobaseBiocGenericsBiocParallelBiostringsbitopscigarillocodetoolscpp11crayonDelayedArraydeldirformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangeshwriterinterpIRangesjpeglambda.rlatticelatticeExtraMASSMatrixMatrixGenericsmatrixStatspngpwalignRColorBrewerRcppRcppEigenRhtslibRsamtoolsS4ArraysS4VectorsSeqinfoShortReadsnowSparseArraySummarizedExperimentXVector

Simulating ChIP-seq experiments

Rendered fromChIPsimIntro.Rnwusingutils::Sweaveon Jun 19 2026.

Last update: 2013-11-01
Started: 2013-11-01

Readme and manuals

Help Manual

Help pageTopics
Simulation of ChIP-seq experimentsChIPsim-package ChIPsim
Convert a feature density into a read densitybindDens2readDens
Conversion between numerical and ASCII representation of read qualitiesdecodeQuality encodeQuality
Default parameters for simChIPdefaultControl
Replacement probabilities for sequencing errorsdefaultErrorProb
Default functions for simChIPdefaultFunctions
Defaults for Feature GeneratordefaultGenerator defaultInit defaultLastFeat defaultTransition
Obtain read qualities from a Fastq file or ShortReadQ objectextractQuality
Convert a list of features into a feature densityfeat2dens
Computing density for a given featurefeatureDensity featureDensity.FuzzyFeature featureDensity.NFRFeature featureDensity.ReversePhasedFeature featureDensity.StableFeature featureDensity.StablePhasedFeature
Generating FeaturesfuzzyFeature nfrFeature phasedFeature stableFeature
Generating a list of genomic featuresmakeFeatures
Generating and reconciling a feature sequenceplaceFeatures
Convert read positions to fastq recordspos2fastq
Introduce errors into read sequence based on quality scoresreadError
Sample read qualities from a listreadQualitySample
Convert read position into read sequencereadSequence
Post-processing of simulated featuresreconcileFeatures reconcileFeatures.default reconcileFeatures.NucleosomePosition reconcileFeatures.SimulatedExperiment
Sampling sequence read positions from a read density.sampleReads
Simulate ChIP-seq experimentssimChIP
Generate unique read namessimpleNames
Write read sequences and qualities to a FASTQ formatted filewriteFASTQ
Create fastq file from read positionswriteReads