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MotifPeeker
This is thereleased version of MotifPeeker; for the devel version, seeMotifPeeker.
Benchmarking Epigenomic Profiling Methods Using Motif Enrichment
Bioconductor version: Release (3.22)
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("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 appropriateBioconductor 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 | 1.2.0 |
| 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,Seqinfo,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
FollowInstallation instructions to use this package in your R session.
| Source Package | MotifPeeker_1.2.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | MotifPeeker_1.2.0.tgz |
| macOS Binary (arm64) | MotifPeeker_1.2.0.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 |