TFutils

DOI: 10.18129/B9.bioc.TFutils  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see TFutils.

TFutils

Bioconductor version: 3.16

This package helps users to work with TF metadata from various sources. Significant catalogs of TFs and classifications thereof are made available. Tools for working with motif scans are also provided.

Author: Vincent Carey [aut, cre], Shweta Gopaulakrishnan [aut]

Maintainer: Vincent Carey <stvjc at channing.harvard.edu>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("TFutils")

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("TFutils")

 

HTML	R Script	A note on fimo16
HTML	R Script	TFutils -- representing TFBS and TF target sets
PDF		Reference Manual
Text		NEWS

Details

biocViews	Software, Transcriptomics
Version	1.18.0
In Bioconductor since	BioC 3.7 (R-3.5) (5 years)
License	Artistic-2.0
Depends	R (>= 4.1.0)
Imports	methods, dplyr, magrittr, miniUI, shiny, Rsamtools, GSEABase, rjson, BiocFileCache, DT, httr, readxl, AnnotationDbi, org.Hs.eg.db, utils
LinkingTo
Suggests	knitr, data.table, testthat, AnnotationFilter, Biobase, GenomicFeatures, GenomicRanges, Gviz, IRanges, S4Vectors, EnsDb.Hsapiens.v75, BiocParallel, BiocStyle, GO.db, GenomicFiles, GenomeInfoDb, SummarizedExperiment, UpSetR, ggplot2, png, gwascat, MotifDb, motifStack, RColorBrewer, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	TFutils_1.18.0.tar.gz
Windows Binary	TFutils_1.18.0.zip
macOS Binary (x86_64)	TFutils_1.18.0.tgz
macOS Binary (arm64)	TFutils_1.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TFutils
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TFutils
Bioc Package Browser	https://code.bioconductor.org/browse/TFutils/
Package Short Url	https://bioconductor.org/packages/TFutils/
Package Downloads Report	Download Stats