Package: ChIPsim 1.59.0

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

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ChIPsim.pdf |ChIPsim.html✨
ChIPsim/json (API)

# Install 'ChIPsim' in R:

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

On BioConductor:ChIPsim-1.59.0(bioc 3.20)ChIPsim-1.58.0(bioc 3.19)

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

bioconductor-package

40 exports 1.24 score 54 dependencies 1 mentions

Last updated 2 months agofrom:0f3731ad8e

Exports:bindDens2readDens bindLocDens decodeQuality defaultControl defaultErrorProb defaultFunctions defaultGenerator defaultInit defaultLastFeat defaultTransition distDens encodeQuality extractQuality feat2dens featureDensity fragDens fuzzyFeature indNuc joinRegion makeFeatures nfrFeature noNuc phasedFeature phaseNuc placeFeatures pos2fastq readError readQualitySample readSequence reconcileFeatures sampleFromFile sampleReads simChIP simpleNames solexaNames stableDens stableFeature writeFASTQ writeIllumina writeReads

Dependencies:abind askpass BH Biobase BiocGenerics BiocParallel Biostrings bitops codetools cpp11 crayon curl DelayedArray deldir formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges httr hwriter interp IRanges jpeg jsonlite lambda.r lattice latticeExtra MASS Matrix MatrixGenerics matrixStats mime openssl png pwalign R6 RColorBrewer Rcpp RcppEigen Rhtslib Rsamtools S4Arrays S4Vectors ShortRead snow SparseArray SummarizedExperiment sys UCSC.utils XVector zlibbioc

Simulating ChIP-seq experiments

Rendered fromChIPsimIntro.Rnwusingutils::Sweaveon Jul 03 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

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