ChIPanalyser
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ChIPanalyser.
ChIPanalyser: Predicting Transcription Factor Binding Sites
Bioconductor version: 3.9
Based on a statistical thermodynamic framework, ChIPanalyser tries to produce ChIP-seq like profile. The model relies on four consideration: TF binding sites can be scored using a Position weight Matrix, DNA accessibility plays a role in Transcription Factor binding, binding profiles are dependant on the number of transcription factors bound to DNA and finally binding energy (another way of describing PWM's) or binding specificity should be modulated (hence the introduction of a binding specificity modulator). The end result of ChIPanalyser is to produce profiles simulating real ChIP-seq profile and provide accuracy measurements of these predicted profiles after being compared to real ChIP-seq data. The ultimate goal is to produce ChIP-seq like profiles predicting ChIP-seq like profile to circumvent the need to produce costly ChIP-seq experiments.
Author: Patrick C.N.Martin & Nicolae Radu Zabet
Maintainer: Patrick C.N. Martin <pm16057 at essex.ac.uk>
citation("ChIPanalyser")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ChIPanalyser")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ChIPanalyser")| ChIPanalyser User's Guide | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, BiologicalQuestion, ChIPSeq, ChipOnChip, Coverage, DataImport, PeakDetection, SequenceMatching, Sequencing, Software, Transcription, WorkflowStep |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (6.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.5.0), GenomicRanges, Biostrings, BSgenome, RcppRoll, parallel |
| Imports | methods, IRanges, S4Vectors, grDevices, graphics, stats, utils, rtracklayer, ROCR, BiocManager, GenomeInfoDb |
| System Requirements | |
| URL |
See More
| Suggests | BSgenome.Dmelanogaster.UCSC.dm3, knitr, RUnit, BiocGenerics |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ChIPanalyser_1.6.0.tar.gz |
| Windows Binary | ChIPanalyser_1.6.0.zip |
| Mac OS X 10.11 (El Capitan) | ChIPanalyser_1.6.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ChIPanalyser |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ChIPanalyser |
| Bioc Package Browser | https://code.bioconductor.org/browse/ChIPanalyser/ |
| Package Short Url | https://bioconductor.org/packages/ChIPanalyser/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |