ChIPanalyser
This is the released version of ChIPanalyser; for the devel version, see ChIPanalyser.
ChIPanalyser: Predicting Transcription Factor Binding Sites
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | |
| 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 | 1.34.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (9 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_1.34.0.tar.gz |
| Windows Binary (x86_64) | ChIPanalyser_1.34.0.zip |
| macOS Binary (big-sur-x86_64) | ChIPanalyser_1.34.0.tgz |
| macOS Binary (sonoma-arm64) | ChIPanalyser_1.34.0.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 |