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Bioconductor - MotifPeeker

MotifPeeker

This is the released version of MotifPeeker; for the devel version, see MotifPeeker.

Benchmarking Epigenomic Profiling Methods Using Motif Enrichment

Bioconductor version: Release (3.21)

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] ORCID: 0009-0005-5514-505X , Thomas Roberts [aut] ORCID: 0009-0006-6244-8670 , Maria Weinert [aut] ORCID: 0000-0001-6187-1000 , Nathan Skene [aut] ORCID: 0000-0002-6807-3180

Maintainer: Hiranyamaya Dash <hdash.work at gmail.com>

Citation (from within R, enter 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")

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) (< 6 months) 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 Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

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

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