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TFutils

TFutils

Bioconductor version: Release (3.17)

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 "4.3") 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

Details

biocViews Software, Transcriptomics
Version 1.20.0
In Bioconductor since BioC 3.7 (R-3.5) (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
Linking To
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
System Requirements
Enhances
URL
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Depends On Me
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Package Archives

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

Source Package TFutils_1.20.0.tar.gz
Windows Binary TFutils_1.20.0.zip
macOS Binary (x86_64) TFutils_1.20.0.tgz
macOS Binary (arm64) TFutils_1.20.0.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