Package: MotifPeeker 1.5.0

Hiranyamaya Dash

MotifPeeker: Benchmarking Epigenomic Profiling Methods Using Motif Enrichment

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.

Authors:Hiranyamaya Dash [cre, aut], Thomas Roberts [aut], Maria Weinert [aut], Nathan Skene [aut]

MotifPeeker_1.5.0.tar.gz
MotifPeeker_1.5.0.zip(r-4.7)MotifPeeker_1.5.0.zip(r-4.6)MotifPeeker_1.5.0.zip(r-4.5)
MotifPeeker_1.5.0.tgz(r-4.6-any)MotifPeeker_1.5.0.tgz(r-4.5-any)
MotifPeeker_1.5.0.tar.gz(r-4.7-any)MotifPeeker_1.5.0.tar.gz(r-4.6-any)
MotifPeeker_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MotifPeeker/json (API)

# Install 'MotifPeeker' in R:

install.packages('MotifPeeker', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/neurogenomics/motifpeeker/issues

Datasets:

CTCF_ChIP_peaks - Example ChIP-seq peak file
CTCF_TIP_peaks - Example TIP-seq peak file
motif_MA1102.3 - Example CTCFL JASPAR motif file
motif_MA1930.2 - Example CTCF JASPAR motif file

On BioConductor:MotifPeeker-1.5.0(bioc 3.24)MotifPeeker-1.4.0(bioc 3.23)

epigenetics genetics qualitycontrol chipseq multiplecomparison functionalgenomics motifdiscovery sequencematching software alignment bioconductor bioconductor-package chip-seq epigenomics interactive-report motif-enrichment-analysis

5.38 score 2 stars 7 scripts 20 exports 173 dependencies

Last updated from:09c90284ea. Checks:1 WARNING, 6 OK, 3 ERROR. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	400
linux-devel-x86_64	OK	710
source / vignettes	OK	560
linux-release-x86_64	OK	651
macos-release-arm64	OK	316
macos-oldrel-arm64	OK	372
windows-devel	ERROR	544
windows-release	ERROR	518
windows-oldrel	ERROR	502
wasm-release	OK	391

Exports:%>%bootstrap_distances calc_frip check_ENCODE check_genome_build check_JASPAR denovo_motifs find_motifs get_df_distances get_df_distances_bootstrapped get_df_enrichment get_JASPARCORE motif_enrichment motif_similarity MotifPeeker read_motif_file read_peak_file save_peak_file segregate_seqs summit_to_motif

Dependencies:abind askpass assertthat base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob brio BSgenome bslib ca cachem callr cigarillo cli clipr cluster cmdfun codetools colorspace cpp11 crayon credentials crosstalk curl data.table DBI dbplyr DelayedArray dendextend desc diffobj digest dplyr DT egg evaluate farver fastmap filelock fontawesome foreach formatR fs futile.logger futile.options gclus generics GenomicAlignments GenomicRanges gert ggplot2 gitcreds glue gridExtra gtable heatmaply highr hms htmltools htmlwidgets httr httr2 ini IRanges isoband iterators jquerylib jsonlite knitr labeling lambda.r later lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memes memoise mgcv mime nlme openssl otel patchwork permute pillar pkgbuild pkgconfig pkgload plotly plyr praise prettyunits processx progress promises ps purrr qap R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppThread RCurl readr registry reshape2 restfulr Rhtslib rjson rlang rmarkdown rprojroot Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo seriation snow SparseArray stringi stringr SummarizedExperiment sys testthat tibble tidyr tidyselect tinytex TSP tzdb universalmotif usethis utf8 vctrs vegan viridis viridisLite vroom waldo webshot whisker withr xfun XML xml2 XVector yaml zip

Get started

Rendered fromMotifPeeker.Rmdusingknitr::rmarkdown

Last update: 2025-11-20
Started: 2024-07-10

Troubleshooting

Rendered fromtroubleshooting.Rmdusingknitr::rmarkdown

Last update: 2024-11-12
Started: 2024-07-11

Help page	Topics
Bootstrap motif-summit distances for one set of peaks and one motif	bootstrap_distances
Calculate FRiP score	calc_frip
Check for ENCODE input	check_ENCODE
Check genome build	check_genome_build
Check for JASPAR input	check_JASPAR
Example ChIP-seq peak file	CTCF_ChIP_peaks
Example TIP-seq peak file	CTCF_TIP_peaks
Discover motifs in sequences	denovo_motifs
Find similar motifs	find_motifs
Get dataframe with motif-summit distances	get_df_distances
Get dataframe with bootstrapped motif-summit distances	get_df_distances_bootstrapped
Get dataframe with motif enrichment values	get_df_enrichment
Download JASPAR CORE database	get_JASPARCORE
Calculate motif enrichment in a set of sequences	motif_enrichment
Example CTCFL JASPAR motif file	motif_MA1102.3
Example CTCF JASPAR motif file	motif_MA1930.2
Compare motifs from segregated sequences	motif_similarity
Benchmark epigenomic profiling methods using motif enrichment	MotifPeeker
Read a motif file	read_motif_file
Read MACS2/3 narrowPeak or SEACR BED peak file	read_peak_file
Minimally save a peak object to a file (BED4)	save_peak_file
Segregate input sequences into common and unique groups	segregate_seqs
Calculate the distance between peak summits and motifs	summit_to_motif

Package: MotifPeeker 1.5.0

MotifPeeker: Benchmarking Epigenomic Profiling Methods Using Motif Enrichment

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