ChIPanalyser
This is the development version of ChIPanalyser; for the stable release version, see ChIPanalyser.
ChIPanalyser: Predicting Transcription Factor Binding Sites
Bioconductor version: Development (3.21)
ChIPanalyser is a package to predict and understand TF binding by utilizing a statistical thermodynamic model. The model incorporates 4 main factors thought to drive TF binding: Chromatin State, Binding energy, Number of bound molecules and a scaling factor modulating TF binding affinity. Taken together, ChIPanalyser produces ChIP-like profiles that closely mimic the patterns seens in real ChIP-seq data.
Author: Patrick C.N.Martin & Nicolae Radu Zabet
Maintainer: Patrick C.N. Martin <pcnmartin at gmail.com>
citation("ChIPanalyser")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | |
| ChIPanalyser User's Guide for Genetic Algorithms | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, BiologicalQuestion, ChIPSeq, ChipOnChip, Coverage, DataImport, PeakDetection, SequenceMatching, Sequencing, Software, Transcription, WorkflowStep |
| Version | 1.29.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (7 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, RColorBrewer |
| System Requirements | |
| URL |
See More
| Suggests | BSgenome.Dmelanogaster.UCSC.dm6, 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_1.29.0.tar.gz |
| Windows Binary (x86_64) | ChIPanalyser_1.29.0.zip (64-bit only) |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |