Learn R Programming

ChIPsim

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.

Installation

Both the development and release version of this R package are available through Bioconductor. Use the BiocInstaller to install the package and its dependencies from within R.

source("http://bioconductor.org/biocLite.R")
biocLite("ChIPseqR")

Copy Link

Version

Version

1.26.0

License

GPL (>= 2)

Maintainer

Peter Humburg

Last Published

February 15th, 2017

Functions in ChIPsim (1.26.0)

Conversion between numerical and ASCII representation of read qualities

ChIPsim-package

Simulation of ChIP-seq experiments

Generating a list of genomic features

defaultFunctions

Default functions for simChIP

reconcileFeatures

Post-processing of simulated features

Internal and undocumented functions

FeatureGenerators

Generating Features

Obtain read qualities from a Fastq file or ShortReadQ object

Convert read positions to fastq records

Generating and reconciling a feature sequence

Computing densities for nucleosome positioning simulation

Computing density for a given feature

defaultGenerator

Defaults for Feature Generator

Sampling sequence read positions from a read density.

Write read sequences and qualities to a FASTQ formatted file

defaultErrorProb

Replacement probabilities for sequencing errors

Combining two feature densities

readQualitySample

Sample read qualities from a list

bindDens2readDens

Convert a feature density into a read density

Create fastq file from read positions

Simulate ChIP-seq experiments

Introduce errors into read sequence based on quality scores

Convert read position into read sequence

Convert a list of features into a feature density

Default parameters for simChIP

Generate unique read names