MotifPeeker
This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see MotifPeeker.
Benchmarking Epigenomic Profiling Methods Using Motif Enrichment
Bioconductor version: 3.21
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. De-Novo Motif Enrichment Analysis) Statistics for the frequency of de-novo 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")):
Installation
To install this package, start R (version "4.5") 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 | 1.0.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (0.5 years) |
| License | GPL (>= 3) |
| Depends | R (>= 4.4.0) |
| Imports | BiocFileCache, BiocParallel, DT, ggplot2, plotly, universalmotif, GenomicRanges, IRanges, rtracklayer, tools, htmltools, rmarkdown, viridis, SummarizedExperiment, htmlwidgets, Rsamtools, GenomicAlignments, GenomeInfoDb, Biostrings, BSgenome, memes, S4Vectors, dplyr, purrr, tidyr, heatmaply, stats, utils |
| System Requirements | MEME Suite (v5.3.3 or above) |
| 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, 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MotifPeeker_1.0.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | MotifPeeker_1.0.0.tgz |
| macOS Binary (arm64) | MotifPeeker_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MotifPeeker |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MotifPeeker |
| Bioc Package Browser | https://code.bioconductor.org/browse/MotifPeeker/ |
| Package Short Url | https://bioconductor.org/packages/MotifPeeker/ |
| Package Downloads Report | Download Stats |