TFutils

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

TFutils

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DOI: 10.18129/B9.bioc.TFutils

Bioconductor version: Release (3.22)

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")):

Installation

To install this package, start R (version "4.5") 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 1.30.0

In Bioconductor since BioC 3.7 (R-3.5) (7.5 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

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Package Archives

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

Source Package TFutils_1.30.0.tar.gz

Windows Binary (x86_64) TFutils_1.29.1.zip

macOS Binary (x86_64) TFutils_1.30.0.tgz

macOS Binary (arm64) TFutils_1.30.0.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/

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