TFutils

This is the released version of TFutils; for the devel version, see TFutils.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7

TFutils

Bioconductor version: Release (3.23)

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>

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

Vincent Carey, Shweta Gopaulakrishnan. TFutils: TFutils. doi:10.18129/B9.bioc.TFutils, R package version 1.32.0, https://bioconductor.org/packages/TFutils.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Software, Transcriptomics
Version	1.32.0
In Bioconductor since	BioC 3.7 (R-3.5) (8.5 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, GenomicFiles, SummarizedExperiment
System Requirements
URL

Suggests	knitr, data.table, testthat, AnnotationFilter, Biobase, GenomicFeatures, GenomicRanges, Gviz, IRanges, S4Vectors, EnsDb.Hsapiens.v75, BiocParallel, BiocStyle, GO.db, Seqinfo, UpSetR, ggplot2, png, gwascat, MotifDb, motifStack, RColorBrewer, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	TFutils_1.32.0.tar.gz
Windows Binary (x86_64)	TFutils_1.32.0.zip
macOS Binary (big-sur-x86_64)	TFutils_1.32.0.tgz
macOS Binary (sonoma-arm64)	TFutils_1.32.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TFutils
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TFutils
Package Short Url	https://bioconductor.org/packages/TFutils/
Package Downloads Report	Download Stats