Package: ChIPsim 1.67.0

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_1.67.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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-1.67.0(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.

infrastructure chipseq

4.00 score 5 scripts 1 mentions 40 exports 45 dependencies

Last updated from:2272baef61. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	233
linux-devel-x86_64	NOTE	338
source / vignettes	OK	282
linux-release-x86_64	NOTE	355
macos-release-arm64	NOTE	170
macos-oldrel-arm64	NOTE	164
windows-devel	NOTE	224
windows-release	NOTE	223
windows-oldrel	NOTE	231
wasm-release	OK	161

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 BH Biobase BiocGenerics BiocParallel Biostrings bitops cigarillo codetools cpp11 crayon DelayedArray deldir formatR futile.logger futile.options generics GenomicAlignments GenomicRanges hwriter interp IRanges jpeg lambda.r lattice latticeExtra MASS Matrix MatrixGenerics matrixStats png pwalign RColorBrewer Rcpp RcppEigen Rhtslib Rsamtools S4Arrays S4Vectors Seqinfo ShortRead snow SparseArray SummarizedExperiment XVector

Simulating ChIP-seq experiments

Rendered fromChIPsimIntro.Rnwusingutils::Sweave

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