MotifPeeker
This is the released version of MotifPeeker; for the devel version, see MotifPeeker.
Benchmarking Epigenomic Profiling Methods Using Motif Enrichment
Bioconductor version: Release (3.23)
MotifPeeker is used to compare and analyse datasets from epigenomic profiling methods with motif enrichment as the key benchmark. The package outputs an HTML report consisting of three sections: (1. General Metrics) Overview of peaks-related general metrics for the datasets (FRiP scores, peak widths and motif-summit distances). (2. Known Motif Enrichment Analysis) Statistics for the frequency of user-provided motifs enriched in the datasets. (3. Motif Discovery Enrichment Analysis) Statistics for the frequency of ab-initio discovered motifs enriched in the datasets and compared with known motifs.
Author: Hiranyamaya Dash [cre, aut] 
, Thomas Roberts [aut] , Maria Weinert [aut] , Nathan Skene [aut]
Maintainer: Hiranyamaya Dash <hdash.work at gmail.com>
citation("MotifPeeker")):Hiranyamaya Dash, Thomas Roberts, Maria Weinert, Nathan Skene. MotifPeeker: Benchmarking Epigenomic Profiling Methods Using Motif Enrichment. doi:10.18129/B9.bioc.MotifPeeker, R package version 1.4.0, https://bioconductor.org/packages/MotifPeeker.
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("MotifPeeker")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("MotifPeeker")| MotifPeeker | HTML | R Script |
| troubleshooting | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| INSTALL | Text |
Details
| biocViews | Alignment, ChIPSeq, Epigenetics, FunctionalGenomics, Genetics, MotifDiscovery, MultipleComparison, QualityControl, SequenceMatching, Software |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 years) |
| License | GPL (>= 3) |
| Depends | R (>= 4.5.0) |
| Imports | BiocFileCache, BiocParallel, DT, ggplot2, plotly, universalmotif, GenomicRanges, IRanges, rtracklayer, tools, htmltools, rmarkdown, viridis, SummarizedExperiment, htmlwidgets, Rsamtools, GenomicAlignments, Seqinfo, Biostrings, BSgenome, memes, S4Vectors, dplyr, purrr, tidyr, heatmaply, stats, utils |
| System Requirements | MEME Suite (v5.3.3 or above) <http://meme-suite.org/doc/download.html> |
| URL | https://github.com/neurogenomics/MotifPeeker |
| Bug Reports | https://github.com/neurogenomics/MotifPeeker/issues |
See More
| Suggests | BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm39, downloadthis, knitr, markdown, methods, remotes, rworkflows, testthat (>= 3.0.0), withr, emoji, curl, jsonlite |
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| Enhances | |
| Depends On Me | |
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| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MotifPeeker_1.4.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | MotifPeeker_1.4.0.tgz |
| macOS Binary (sonoma-arm64) | MotifPeeker_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MotifPeeker |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MotifPeeker |
| Package Short Url | https://bioconductor.org/packages/MotifPeeker/ |
| Package Downloads Report | Download Stats |