target

This is the development version of target; for the stable release version, see target.

Predict Combined Function of Transcription Factors

Bioconductor version: Development (3.24)

Implement the BETA algorithm for infering direct target genes from DNA-binding and perturbation expression data Wang et al. (2013) . Extend the algorithm to predict the combined function of two DNA-binding elements from comprable binding and expression data.

Author: Mahmoud Ahmed [aut, cre]

Maintainer: Mahmoud Ahmed <mahmoud.s.fahmy at students.kasralainy.edu.eg>

Citation (from within R, enter citation("target")):

Seminal Bioconductor project articles:

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")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("target")

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("target")

Using target to predict combined binding	HTML	R Script
Using the target package	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Software, StatisticalMethod, Transcription
Version	1.27.0
In Bioconductor since	BioC 3.10 (R-3.6) (7 years)
License	GPL-3
Depends	R (>= 3.6)
Imports	BiocGenerics, GenomicRanges, IRanges, matrixStats, methods, stats, graphics, shiny
System Requirements
URL	https://github.com/MahShaaban/target
Bug Reports	https://github.com/MahShaaban/target/issues

Suggests	testthat (>= 2.1.0), knitr, rmarkdown, shinytest, shinyBS, covr
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	target_1.27.0.tar.gz
Windows Binary (x86_64)	target_1.27.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	target_1.27.0.tgz
macOS Binary (sonoma-arm64)	target_1.27.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/target
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/target
Bioc Package Browser	https://code.bioconductor.org/browse/target/
Package Short Url	https://bioconductor.org/packages/target/
Package Downloads Report	Download Stats