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

MotifPeeker HTML R Script

troubleshooting HTML R Script

Reference Manual PDF

NEWS Text

INSTALL Text

Need some help? Ask on the Bioconductor Support site!

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

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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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/

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