Bioconductor - motifTestR
Bioconductor 3.22
Software Packages
motifTestR
motifTestR
This is the
released
version of motifTestR; for the devel version, see
motifTestR
Perform key tests for binding motifs in sequence data
DOI:
10.18129/B9.bioc.motifTestR
Bioconductor version:
Release (3.22)
Taking a set of sequence motifs as PWMs, test a set of sequences for over-representation of these motifs, as well as any positional features within the set of motifs. Enrichment analysis can be undertaken using multiple statistical approaches. The package also contains core functions to prepare data for analysis, and to visualise results.
Author:
Stevie Pederson [aut, cre]
ORCID: 0000-0001-8197-3303
Maintainer:
Stevie Pederson
Citation (from within R, enter
citation("motifTestR")
):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("motifTestR")
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("motifTestR")
Motif Analysis Using motifTestR
HTML
R Script
Reference Manual
PDF
NEWS
Text
Need some help? Ask on the Bioconductor Support site!
Details
biocViews
ChIPSeq
ChipOnChip
MotifAnnotation
SequenceMatching
Software
Version
1.6.1
In Bioconductor since
BioC 3.19 (R-4.4) (2 years)
License
GPL-3
Depends
Biostrings
GenomicRanges
ggplot2
(>= 4.0.0), R (>= 4.5.0)
Imports
Seqinfo
, graphics,
harmonicmeanp
IRanges
matrixStats
, methods, parallel,
patchwork
rlang
S4Vectors
, stats,
universalmotif
System Requirements
URL
Bug Reports
See More
Suggests
AnnotationHub
BiocStyle
BSgenome.Hsapiens.UCSC.hg19
extraChIPs
(>= 1.13.3),
ggdendro
knitr
MASS
MotifDb
rmarkdown
rtracklayer
SimpleUpset
testthat
(>= 3.0.0),
VGAM
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
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Build Report
Package Archives
Follow
Installation
instructions to use this package in your R session.
Source Package
motifTestR_1.6.1.tar.gz
Windows Binary (x86_64)
motifTestR_1.6.1.zip
(64-bit only)
macOS Binary (x86_64)
motifTestR_1.6.1.tgz
macOS Binary (arm64)
motifTestR_1.6.1.tgz
Source Repository
git clone https://git.bioconductor.org/packages/motifTestR
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/motifTestR
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