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.

Author
Peter Humburg
Date of publication
None
Maintainer
Peter Humburg <Peter.Humburg@gmail.com>
License
GPL (>= 2)
Version
1.28.0

View on Bioconductor

Man pages

bindDens2readDens
Convert a feature density into a read density
ChIPsim-package
Simulation of ChIP-seq experiments
decodeQuality
Conversion between numerical and ASCII representation of read...
defaultControl
Default parameters for simChIP
defaultErrorProb
Replacement probabilities for sequencing errors
defaultFunctions
Default functions for simChIP
defaultGenerator
Defaults for Feature Generator
distDens
Computing densities for nucleosome positioning simulation
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
internal
Internal and undocumented functions
joinRegion
Combining two feature densities
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

Files in this package

ChIPsim/DESCRIPTION
ChIPsim/NAMESPACE
ChIPsim/R
ChIPsim/R/nucSim.R
ChIPsim/README.md
ChIPsim/build
ChIPsim/build/vignette.rds
ChIPsim/inst
ChIPsim/inst/doc
ChIPsim/inst/doc/ChIPsimIntro.R
ChIPsim/inst/doc/ChIPsimIntro.Rnw
ChIPsim/inst/doc/ChIPsimIntro.pdf
ChIPsim/man
ChIPsim/man/ChIPsim-package.Rd
ChIPsim/man/bindDens2readDens.Rd
ChIPsim/man/decodeQuality.Rd
ChIPsim/man/defaultControl.Rd
ChIPsim/man/defaultErrorProb.Rd
ChIPsim/man/defaultFunctions.Rd
ChIPsim/man/defaultGenerator.Rd
ChIPsim/man/distDens.Rd
ChIPsim/man/extractQuality.Rd
ChIPsim/man/feat2dens.Rd
ChIPsim/man/featureDensity.Rd
ChIPsim/man/internal.Rd
ChIPsim/man/joinRegion.Rd
ChIPsim/man/makeFeatures.Rd
ChIPsim/man/placeFeatures.Rd
ChIPsim/man/pos2fastq.Rd
ChIPsim/man/readError.Rd
ChIPsim/man/readQualitySample.Rd
ChIPsim/man/readSequence.Rd
ChIPsim/man/reconcileFeatures.Rd
ChIPsim/man/sampleReads.Rd
ChIPsim/man/simChIP.Rd
ChIPsim/man/simpleNames.Rd
ChIPsim/man/stableFeature.Rd
ChIPsim/man/writeFASTQ.Rd
ChIPsim/man/writeReads.Rd
ChIPsim/vignettes
ChIPsim/vignettes/ChIPsimIntro.Rnw