Package: universalmotif 1.31.37
Benjamin Jean-Marie Tremblay
universalmotif: Import, Modify, and Export Motifs with R
A comprehensive toolkit for working with sequence motifs in R. Imports and exports most common motif formats (JASPAR, MEME, HOMER, TRANSFAC, CIS-BP, UNIPROBE) and interoperates with the other Bioconductor motif packages. Analysis functions cover de novo motif discovery, motif-vs-motif comparison and clustering, P-value calculation, sequence scanning, enrichment against shuffled or composition-matched backgrounds, positional bias testing, and pairwise motif co-occurrence. Also includes utilities for sequence shuffling, motif trimming, higher-order representations, ground-truth simulation by motif implantation, and logo-plotting functionality.
Authors:
universalmotif_1.31.37.tar.gz
universalmotif_1.31.37.zip(r-4.7)universalmotif_1.31.37.zip(r-4.6)universalmotif_1.31.37.zip(r-4.5)
universalmotif_1.31.37.tgz(r-4.6-x86_64)universalmotif_1.31.37.tgz(r-4.6-arm64)universalmotif_1.31.37.tgz(r-4.5-x86_64)universalmotif_1.31.37.tgz(r-4.5-arm64)
universalmotif_1.31.37.tar.gz(r-4.7-arm64)universalmotif_1.31.37.tar.gz(r-4.7-x86_64)universalmotif_1.31.37.tar.gz(r-4.6-arm64)universalmotif_1.31.37.tar.gz(r-4.6-x86_64)
universalmotif_1.31.37.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
universalmotif/json (API)
NEWS
| # Install 'universalmotif' in R: |
| install.packages('universalmotif', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bjmt/universalmotif/issues
- ArabidopsisMotif - Arabidopsis motif in 'universalmotif' format.
- ArabidopsisPromoters - Arabidopsis promoters as a 'DNAStringSet'.
- examplemotif - Example motif in 'universalmotif' format.
- examplemotif2 - Another example motif in 'universalmotif' format.
- fontDFroboto - Polygon coordinates for plotting letters.
- JASPAR2018_CORE_DBSCORES - JASPAR2018 CORE database scores
On BioConductor:universalmotif-1.31.32(bioc 3.24)universalmotif-1.30.1(bioc 3.23)
motifannotationmotifdiscoverydataimportgeneregulationmotif-analysismotif-enrichment-analysissequence-logocpp
Last updated from:f7d995f9c3. Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 328 | ||
| linux-devel-arm64 | WARNING | 831 | ||
| linux-devel-x86_64 | WARNING | 749 | ||
| source / vignettes | OK | 613 | ||
| linux-release-arm64 | WARNING | 615 | ||
| linux-release-x86_64 | WARNING | 684 | ||
| macos-release-arm64 | WARNING | 356 | ||
| macos-release-x86_64 | WARNING | 911 | ||
| macos-oldrel-arm64 | WARNING | 453 | ||
| macos-oldrel-x86_64 | WARNING | 1232 | ||
| windows-devel | WARNING | 721 | ||
| windows-release | WARNING | 692 | ||
| windows-oldrel | WARNING | 702 | ||
| wasm-release | OK | 236 |
Exports:add_gapadd_multifreqannotate_logoannotate_motifas.data.frameaverage_iccalc_complexitycalc_windowscbindcolMeanscolnamescolSumscompare_columnscompare_motifscompare_motifs2consensus_to_ppmconsensus_to_ppmAAconvert_motifsconvert_typecount_kletscreate_motifcreate_sequencesdedup_hitsenrich_motifsenrich_motifs2filter_motifsgeom_logogeom_motifGeomMotifget_bkgget_consensusget_consensusAAget_kletsget_matchesget_scoresicm_to_ppmimplant_motifslog_string_pvalmake_DBscoresmask_rangesmask_seqsmatch_bkgmeme_alphmerge_motifsmerge_motifs2merge_similarmerge_similar2motif_cooccmotif_findermotif_peaksmotif_proximitymotif_pvaluemotif_rangemotif_rcmotif_scoremotif_treemotif_tree2ncolnormalizenrowpcm_to_ppmplot_match_bkgplot_motif_peaksplot_motif_proximityposition_icscoreppm_to_icmppm_to_pcmppm_to_pwmprob_matchprob_match_bkgpwm_to_ppmread_cisbpread_homerread_jasparread_matrixread_memeread_motifsread_transfacread_uniproberequires_updateround_motifrowMeansrownamesrowSumsrun_memesample_sitesscan_sequencesscan_sequences2score_matchsequence_complexityshuffle_motifsshuffle_sequencesshuffle_stringslide_funStatLogoStatMotifsubsetsummarise_motifsswitch_alphto_dfto_listtrim_cwmtrim_motifsungapupdate_motifsview_logoview_motifsview_motifs2window_stringwrite_homerwrite_jasparwrite_matrixwrite_memewrite_motifswrite_transfac
Dependencies:BiocGenericsBiostringsclicpp11crayonfarvergenericsggplot2gluegtableIRangesisobandlabelinglifecycleMASSMatrixGenericsmatrixStatsR6RColorBrewerRcppRcppThreadrlangS4VectorsS7scalesSeqinfovctrsviridisLitewithrXVectoryaml
An end-to-end ChIP-seq workflow: from a peak BED to enriched motifs
Rendered fromChIPseqWorkflow.Rmdusingknitr::rmarkdownon Jun 08 2026.Last update: 2026-05-30
Started: 2026-05-25
Building a curated motif database from multiple sources
Rendered fromMotifDatabaseCuration.Rmdusingknitr::rmarkdownon Jun 08 2026.Last update: 2026-06-07
Started: 2026-05-26
Introduction to "universalmotif"
Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Jun 08 2026.Last update: 2026-05-05
Started: 2018-08-19
Introduction to sequence motifs
Rendered fromIntroductionToSequenceMotifs.Rmdusingknitr::rmarkdownon Jun 08 2026.Last update: 2026-05-26
Started: 2018-08-19
Motif comparisons and P-values
Rendered fromMotifComparisonAndPvalues.Rmdusingknitr::rmarkdownon Jun 08 2026.Last update: 2026-06-07
Started: 2019-05-26
Motif import, export, and manipulation
Rendered fromMotifManipulation.Rmdusingknitr::rmarkdownon Jun 08 2026.Last update: 2026-05-30
Started: 2018-08-19
Sequence manipulation and scanning
Rendered fromSequenceSearches.Rmdusingknitr::rmarkdownon Jun 08 2026.Last update: 2026-06-08
Started: 2018-08-19
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add multi-letter information to a motif. | add_multifreq |
| Arabidopsis motif in 'universalmotif' format. | ArabidopsisMotif |
| Arabidopsis promoters as a 'DNAStringSet'. | ArabidopsisPromoters |
| Compare motifs. | compare_motifs |
| Faster minimalist motif comparison. | compare_motifs2 |
| Convert motif class. | convert_motifs convert_motifs,AsIs-method convert_motifs,ICMatrix-method convert_motifs,list-method convert_motifs,matrix-method convert_motifs,Motif-method convert_motifs,MotifList-method convert_motifs,pcm-method convert_motifs,pfm-method convert_motifs,PFMatrix-method convert_motifs,PWM-method convert_motifs,pwm-method convert_motifs,PWMatrix-method convert_motifs,TFFMFirst-method convert_motifs,universalmotif-method convert_motifs,XMatrixList-method |
| Convert universalmotif type. | convert_type |
| Create a motif. | create_motif create_motif,AAStringSet-method create_motif,BStringSet-method create_motif,character-method create_motif,DNAStringSet-method create_motif,matrix-method create_motif,missing-method create_motif,numeric-method create_motif,RNAStringSet-method |
| Create random sequences. | create_sequences |
| Deduplicate overlapping motif hits. | dedup_hits |
| Enrich for input motifs in a set of sequences. | enrich_motifs |
| Fast minimalist motif enrichment. | enrich_motifs2 |
| Example motif in 'universalmotif' format. | examplemotif |
| Another example motif in 'universalmotif' format. | examplemotif2 |
| Filter a list of motifs. | filter_motifs |
| Polygon coordinates for plotting letters. | fontDFroboto |
| Embed motif logos in ggplot2 constructions. | annotate_logo annotate_motif GeomMotif geom_logo geom_motif StatLogo StatMotif |
| Calculate sequence background. | get_bkg |
| Implant sampled motif instances into sequences at known positions. | implant_motifs |
| JASPAR2018 CORE database scores | JASPAR2018_CORE_DBSCORES |
| Create P-value databases. | make_DBscores |
| Sample composition-matched background sequences from a universe. | match_bkg |
| Merge motifs. | merge_motifs |
| Merge a list of motifs into a single consensus motif. | merge_motifs2 |
| Identify and merge similar motifs within a collection of motifs (or simply cluster motifs). | merge_similar |
| Cluster similar motifs by significance and merge each cluster. | merge_similar2 |
| Find significantly co-occurring motif pairs in a set of sequences. | motif_coocc |
| Discover _de novo_ motifs in a set of sequences. | motif_finder |
| CentriMo-style positional enrichment of motif hits. | motif_peaks |
| Test for motif enrichment near a set of genomic anchors. | motif_proximity |
| Motif P-value and scoring utility | motif_pvalue |
| Get the reverse complement of a DNA or RNA motif. | motif_rc |
| Generate 'ggplot2' motif trees with 'ggtree'. | motif_tree |
| Generate ggtree-based motif trees using 'compare_motifs2()'. | motif_tree2 |
| Visualise composition match between target and background sequences. | plot_match_bkg |
| Plot the position distribution of motif hits. | plot_motif_peaks |
| Plot the distance-to-anchor distribution of motif hits. | plot_motif_proximity |
| Import CIS-BP motifs. | read_cisbp |
| Import HOMER motifs. | read_homer |
| Import JASPAR motifs. | read_jaspar |
| Import motifs from raw matrices. | read_matrix |
| Import MEME motifs. | read_meme |
| Import universalmotif formatted motifs. | read_motifs |
| Import TRANSFAC motifs. | read_transfac |
| Import UNIPROBE motifs. | read_uniprobe |
| Run MEME from within R. | run_meme |
| Generate binding sites from a motif. | sample_sites |
| Scan sequences for matches to input motifs. | scan_sequences |
| Minimalist motif scanner aligned with yamtk scan defaults. | scan_sequences2 |
| Calculate sequence complexity. | sequence_complexity |
| Shuffle motifs by column. | shuffle_motifs |
| Shuffle input sequences. | shuffle_sequences |
| Switch between DNA and RNA alphabets. | switch_alph |
| Tidy manipulation of motifs. | requires_update tidy-motifs to_df to_list update_motifs |
| Trim CWM motifs by absolute column sum. | trim_cwm |
| Trim motifs. | trim_motifs |
| universalmotif: Motif class. | as.data.frame,universalmotif-method cbind,universalmotif-method colMeans,universalmotif-method colnames,universalmotif-method colSums,universalmotif-method initialize,universalmotif-method ncol,universalmotif-method normalize,universalmotif-method nrow,universalmotif-method rowMeans,universalmotif-method rownames,universalmotif-method rowSums,universalmotif-method show,universalmotif-method subset,universalmotif-method universalmotif universalmotif-class [,universalmotif-method [<-,universalmotif-method |
| universalmotif: Import, Modify and Export Motifs with R | universalmotif-package universalmotif-pkg |
| Utility functions. | utilities |
| Motif-related utility functions. | add_gap average_ic compare_columns consensus_to_ppm consensus_to_ppmAA get_consensus get_consensusAA get_matches get_scores icm_to_ppm log_string_pval motif_range motif_score pcm_to_ppm position_icscore ppm_to_icm ppm_to_pcm ppm_to_pwm prob_match prob_match_bkg pwm_to_ppm round_motif score_match summarise_motifs ungap utils-motif |
| Sequence-related utility functions. | calc_complexity calc_windows count_klets get_klets mask_ranges mask_seqs meme_alph shuffle_string slide_fun utils-sequence window_string |
| Plot logos from numeric matrices. | view_logo |
| Plot motif logos. | view_motifs |
| Plot motif logos using 'compare_motifs2()' alignment (v2). | view_motifs2 |
| Export motifs in HOMER format. | write_homer |
| Export motifs in JASPAR format. | write_jaspar |
| Export motifs as raw matrices. | write_matrix |
| Export motifs in MEME format. | write_meme |
| Export motifs in universalmotif format. | write_motifs |
| Export motifs in TRANSFAC format. | write_transfac |