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ChIPanalyser
This is thereleased version of ChIPanalyser; for the devel version, seeChIPanalyser.
ChIPanalyser: Predicting Transcription Factor Binding Sites
Bioconductor version: Release (3.22)
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")BiocManager::install("ChIPanalyser")For older versions of R, please refer to the appropriateBioconductor 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 | 1.32.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (8 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
FollowInstallation instructions to use this package in your R session.
| Source Package | ChIPanalyser_1.32.0.tar.gz |
| Windows Binary (x86_64) | ChIPanalyser_1.32.0.zip (64-bit only) |
| macOS Binary (x86_64) | ChIPanalyser_1.32.0.tgz |
| macOS Binary (arm64) | ChIPanalyser_1.32.0.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 |