MotifPeeker
Benchmarking Epigenomic Profiling Methods Using Motif Enrichment
Bioconductor version: 3.24 · Package version: 1.5.1
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MotifPeeker")Details
| Maintainer | Hiranyamaya Dash <hdash.work@gmail.com> |
| Author | Hiranyamaya Dash [cre, aut] (ORCID: <https://orcid.org/0009-0005-5514-505X>), Thomas Roberts [aut] (ORCID: <https://orcid.org/0009-0006-6244-8670>), Maria Weinert [aut] (ORCID: <https://orcid.org/0000-0001-6187-1000>), Nathan Skene [aut] (ORCID: <https://orcid.org/0000-0002-6807-3180>) |
| License | GPL (>= 3) |
| URL | https://github.com/neurogenomics/MotifPeeker |
| Bug Reports | https://github.com/neurogenomics/MotifPeeker/issues |
| System Requirements | MEME Suite (v5.3.3 or above) <http://meme-suite.org/doc/download.html> |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alignment, ChIPSeq, Epigenetics, FunctionalGenomics, Genetics, MotifDiscovery, MultipleComparison, QualityControl, SequenceMatching, Software |
| Package Short Url | https://bioconductor.org/packages/MotifPeeker/ |
Citation
From within R, enter 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 1.5.1, https://bioconductor.org/packages/MotifPeeker.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | MotifPeeker_1.5.1.tar.gz |
| macOS binary (arm64) | MotifPeeker_1.5.1.tgz |
| macOS binary (x86_64) | MotifPeeker_1.5.1.tgz |
Dependencies
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
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